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| Status |
Public on Jul 11, 2023 |
| Title |
Decoder-seq enhances mRNA capture efficiency in spatial RNA sequencing |
| Organisms |
Homo sapiens; Mus musculus |
| Experiment type |
Other
Expression profiling by high throughput sequencing
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| Summary |
Here, we report a dendrimeric DNA coordinate barcoding design for spatial RNA sequencing (Decoder-seq) offering both high sensitivity and high resolution.
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| Overall design |
Decoder-seq offers exceptional flexibility and precision in spatial resolution with spot widths of 50, 25, and 15 μm and various capture areas of spatially barcoded arrays. It was employed to mouse hippocampus, olfactory bulb and hemibrain, and human renal cancers.
Please note that [1] the records have been updated with additional HE image files and coordinate file information on Nov 16, 2023 [2] the processed data for GSM7585162 has been updated on Dec 8, 2023.
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| Contributor(s) |
Cao J, Sun D |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
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| Submission date |
Jun 27, 2023 |
| Last update date |
Dec 08, 2023 |
| Contact name |
di sun |
| E-mail(s) |
sundysun9@hotmail.com
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| Organization name |
Renji Hospital, School of Medicine, Shanghai Jiao Tong University
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| Department |
institute of molecular medicine
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| Street address |
pujian road 160
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| City |
shanghai |
| ZIP/Postal code |
200120 |
| Country |
China |
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| Platforms (2) |
| GPL24247 |
Illumina NovaSeq 6000 (Mus musculus) |
| GPL24676 |
Illumina NovaSeq 6000 (Homo sapiens) |
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| Samples (23)
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| GSM7585149 |
clear cell RCC, patient 1, leading-edge [ccRCC-1-L] |
| GSM7585150 |
clear cell RCC, patient 1, tumor core [ccRCC-1-T] |
| GSM7585151 |
chromophobe RCC, patient 1, leading-edge [chRCC-1-L] |
| GSM7585152 |
chromophobe RCC, patient 1, tumor core [chRCC-1-T] |
| GSM7585153 |
clear cell RCC, patient 3, leading-edge [ccRCC-3-L] |
| GSM7585154 |
chromophobe RCC, patient 2, leading-edge [chRCC-2-L] |
| GSM7585155 |
clear cell RCC, patient 2, tumor core [ccRCC-2-T] |
| GSM7585156 |
clear cell RCC, patient 2, leading-edge [ccRCC-2-L] |
| GSM7585157 |
mouse olfactory bulb, 15 μm-spot, rep2 [MOB-15-2] |
| GSM7585158 |
mouse olfactory bulb, 15 μm-spot, rep1 [MOB-15-1] |
| GSM7585159 |
mouse hippocampus, 15 μm-spot [HM-15-1] |
| GSM7585160 |
mouse olfactory bulb, 50 μm-spot, rep1 [MOB-50-1] |
| GSM7585161 |
mouse olfactory bulb, 50 μm-spot, rep2 [MOB-50-2] |
| GSM7585162 |
mouse olfactory bulb, 50 μm-spot, 10x visium [MOB-10x-1] |
| GSM7585163 |
mouse olfactory bulb, ISS, rep1 [MOB-ISS-1] |
| GSM7585164 |
mouse olfactory bulb, ISS, rep2 [MOB-ISS-2] |
| GSM7585165 |
mouse olfactory bulb, ISS, rep3 [MOB-ISS-3] |
| GSM7585166 |
mouse olfactory bulb, 2D amino-modified slides [MOB-50-2D] |
| GSM7585167 |
mouse hemibrain, 50 μm-spot [BRAIN-50-1] |
| GSM7848719 |
mouse olfactory bulb, 15 μm-spot, rep3 [MOB-15-3] |
| GSM7848720 |
mouse olfactory bulb, 50 μm-spot, rep3 [MOB-50-3] |
| GSM7915845 |
mouse olfactory bulb, 50 μm-spot, 3D, slide1 |
| GSM7915846 |
mouse olfactory bulb, 50 μm-spot, 3D, slide2 |
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| Relations |
| BioProject |
PRJNA993105 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE235896_RAW.tar |
1.9 Gb |
(http)(custom) |
TAR (of CSV, H5, JPG, PNG, TAR, TIFF, TXT) |
| GSE235896_barcode.txt.gz |
14.0 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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