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| Status |
Public on Jul 11, 2023 |
| Title |
clear cell RCC, patient 2, leading-edge [ccRCC-2-L] |
| Sample type |
SRA |
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| Source name |
renal cancers
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| Organism |
Homo sapiens |
| Characteristics |
tissue: renal cancers
tissue type: clear cell RCC
subject id: patient 2
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| Extracted molecule |
total RNA |
| Extraction protocol |
Spatial transcriptomic sequencing by Decoder-seq, details in Methods "Dendrimeric DNA coordinate barcoding arrays capture spatial mRNAs of tissues with high efficiency"
Spatial transcriptomic sequencing by Decoder-seq, details in Methods "Amplification, library construction, and sequencing"
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| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
barcode.txt
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| Data processing |
*library strategy: Spatial transcriptomic sequencing
The H&E image was used to accurately distinguish between tissues and backgrounds, with spots outside the tissue being removed. Spots with fewer than 50 observed genes (UMI > 2) were filtered out. And genes with counts in less than 10 spatial spots were discarded. Mitochondrial and ribosomal genes were also removed.
Giotto suite was used to perform spatial gene expression normalization, plotting, dimensionality reduction, spatial domains detection, and differential gene expression analysis. To incorporate spatial information into clustering, we utilized a hidden Markov random field (HMRF) model integrated with Giotto and allocated each cell to one of k spatial domains based on the accepted beta parameter. Furthermore, Giotto's findScanMarkers function was employed to annotate each spatial domain using identified markers.
Assembly: mm10, hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
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| Submission date |
Jul 10, 2023 |
| Last update date |
Nov 16, 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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| Platform ID |
GPL24676 |
| Series (1) |
| GSE235896 |
Decoder-seq enhances mRNA capture efficiency in spatial RNA sequencing |
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| Relations |
| BioSample |
SAMN36381027 |
| SRA |
SRX20960090 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7585156_ccRCC-2-L.bc.intissue.txt.gz |
13.8 Kb |
(ftp)(http) |
TXT |
| GSM7585156_ccRCC-2-L.png.gz |
117.1 Mb |
(ftp)(http) |
PNG |
| GSM7585156_ccRCC-2-L_raw_count.txt.gz |
7.6 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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