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Spatial Gene Expression of Mouse Small Intestine Formalin-fixed Paraffin Embedded Tissue

Stereo-seq N FFPE V1.1, software version: SAW 8.2 & StereoMap 4.2
Stereo-seq OMNI Solution
Mouse Small Intestine Demo Data
Chip SN: Q00517FD
Sample information
Kit information
Experiment information
Sequencing
Analysis result
Input file & Output and supplemental files
Data Details
Sample information
Species : 

Mouse (Strain: C57BL/6; Sex: Male; Age: 6-8 week)

Tissue : 

Small Intestine

Embedding method : 
Formalin-fixed paraffin embedded
DV 200 > 
70%
Kit information
Product : 
Stereo-seq OMNI FFPE
Kit version : 
Stereo-seq N FFPE V1.1
Chip size : 
1 cm × 1 cm
Experiment information
Section thickness : 
5 μm
Staining type : 
ssDNA staining    
Permeabilization time : 
30 min
Sequencing
Total reads : 
1,313,745,902
Sequencer : 
DNBSEQ-G400RS
Analysis result
STOmics Mouse Small Intestine Demo Data Clustering map STOmics Mouse Small Intestine Demo Data Clustering map STOmics Mouse Small Intestine Demo Data Clustering map
Clustering map
  • Analyze Software Version : SAW V8.2, StereoMap V4.2
  • Bin200 Median MID : 42,496

  • Bin200 Median Gene Type : 7,665

  • Bin20 Median MID : 413
  • Bin20 Median Gene Type : 302
  • Cell Bin Gene Type : 243
  • Cell Bin MID : 312
  • Sequencing Saturation : 72.5%

  • Fraction MID in Spots Under Tissue : 87.88%

  • This demo dataset is based on standard SAW results with manual tissue correction and manual Cellbin annotation.


Explore View report
Input files Output and supplemental files
Select All
 Input files Format Size md5sum
Download Selected
V350369392_L01_read_2.fq.gz FQ 14.81GB 3f7ab132b3588c153ff1a48718039e4d
V350369392_L01_read_1.fq.gz FQ 11.92GB d6190aa244d4f08d747eac159a900bdb
V350369279_L02_read_2.fq.gz FQ 12.90GB a0117263125b3506f4b477f9d25afad4
V350369279_L02_read_1.fq.gz FQ 10.74GB 3e1ad785ac8b85630debd2722e8a45d1
V350369279_L01_read_2.fq.gz FQ 13.29GB ccedcbe167c57245363fa1a34fac7966
V350369279_L01_read_1.fq.gz FQ 10.86GB 28147ebe8006b72099ae4b036f6fc015
Q00517FD_SC_20250911_130712_4.2.0.tar.gz TAR 230.75MB 3179c863941bf49306e785452ba95221
Q00517FD_manual_tissue_seg.tif TIFF 1.02MB 705f9b928e392900812d42123e1c3a77
Q00517FD.barcodeToPos.h5 H5 2.73GB 2ec0bd21adda16d0c6c5ee7af6135a7f
Q00517FD_input_command_download TXT
Select All
 Output and supplemental files Format Size md5sum
Download Selected
Q00517FD.visualization.tar.gz TAR 6.05GB bed8d2930a0eaa16d8581edcf8615d52
Q00517FD.tissue.gef GEF 7.33GB 20956c7c3544bef6ae21a5c4566b2522
Q00517FD_ssDNA_regist.tif TIFF 177.07MB 754a2fc9e12a814d18381f9d581d0526
Q00517FD.report.html HTML 73.83MB 34b35808f4ff659f6ec9bac2c88dc453
Q00517FD.raw.gef GEF 1.52GB 892f172f40fe3f1851a4d2b95261bcc2
Q00517FD.cellbin.gef GEF 969.96MB 12615bfd9647fd2e2d959cecc92c96b2
Q00517FD.adjusted.cellbin.gef GEF 1.44GB 4567921b7e8b8160bf76175c30a74897
Q00517FD_output_command_download TXT
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