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Spatial Gene Expression of Mouse Brain Formalin-fixed Paraffin Embedded Tissue

Stereo-seq N FFPE V1.0, software version: SAW 8.1 & StereoMap 4.1
Stereo-seq OMNI Solution
Mouse brain Demo Data
Chip SN: C04138G3
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 : 
Whole Brain
Embedding method : 
Formalin-fixed paraffin embedded    
DV200 : 
＞70%    
Kit information
Product : 
Stereo-seq OMNI FFPE    
Kit version : 
Stereo-seq N FFPE V1.0    
Chip size : 
1 cm × 1 cm
Experiment information
Section thickness : 
5 μm
Staining type : 
H&E staining
Permeabilization time : 
30 min
Sequencing
Total reads : 
3,188,213,166
Sequencer : 
DNBSEQ-T7RS
Analysis result
Heatmap
  • Analyze Software Version : SAW V8.1, StereoMap V4.1
  • Bin200 Median MID : 41,791
  • Bin200 Median Gene Type : 6,174

  • Sequencing Saturation : 78.70%
  • Fraction MID in Spots Under Tissue : 95.61%
  • Manual tissue segmentation was performed.

Explore View report
Input files Output and supplemental files
Select All
 Input files Format Size md5sum
Download Selected
C04138G3_input_command_download TXT 7.13KB 9d6bb4f9f6eee2c6dc4fc4898ad26201
E250018257_L01_104_1.fq.gz FQ 9.61GB 00caf31f15490aba2e9af2d689dc8c8e
E250018257_L01_104_2.fq.gz FQ 17.20GB e537a55a97846da81a8fc9775325b0b7
E250018257_L01_103_1.fq.gz FQ 9.08GB 0a0acbda380b8340896bc476c9d73ddd
E250018257_L01_103_2.fq.gz FQ 16.91GB 7bcb96d6d927161030c61bc2c66ccea7
E250018257_L01_102_1.fq.gz FQ 11.34GB b7bb41142a0c751c565efdf346755a44
E250018257_L01_102_2.fq.gz FQ 20.34GB ea8beb830eb0f20c2fc406c4b0f401d3
E250018257_L01_101_1.fq.gz FQ 10.21GB d64fd72bd4ed432923aeee3b4a8e6789
E250018257_L01_101_2.fq.gz FQ 18.18GB 8cac01fe84ed66226f17b70a51904f9b
E250018257_L01_100_1.fq.gz FQ 492.25MB 003472ca13ad7c717d867db102d6434c
E250018257_L01_100_2.fq.gz FQ 877.98MB 734caef88f4d49f4c15547270a8320f7
E250018257_L01_99_1.fq.gz FQ 5.77GB 40bebee5529ae36f1023268efa6665a2
E250018257_L01_99_2.fq.gz FQ 10.33GB ba85b7e420c03af1dd0374123c2cd974
E250018257_L01_98_1.fq.gz FQ 15.03GB edafade4a092a0ff6ff9bf8ede69285e
E250018257_L01_98_2.fq.gz FQ 26.99GB fb3e79dc9aa18f963069dc76379e1590
E250018257_L01_97_2.fq.gz FQ 12.02GB 0f34a89d642b122eecf675435c1b7644
E250018257_L01_97_1.fq.gz FQ 6.74GB 9085f015181e049e772a42705bd88159
E250018209_L01_8_2.fq.gz FQ 29.40GB 87a200c7fdecf168dca87ebef4d64c95
E250018209_L01_8_1.fq.gz FQ 16.02GB 85b7b32535e8801bc7e98da1b3913fe1
C04138G3_SC_20250306_093009_4.1.2.tar.gz TAR 1.15GB 0bf69b92a10ad8d726d4d47a3daf1bc5
C04138G3.barcodeToPos.h5 H5 2.76GB 7b8e1523cdc5e10f86bea3bafec86022
Select All
 Output and supplemental files Format Size md5sum
Download Selected
C04138G3_output_command_download TXT 2.20KB ded791a84ff9c3c67f0f996b705215ec
C04138G3_HE_regist.tif TIFF 901.48MB d50e169b99f9cf845325e52fe42ddfc7
C04138G3.tissue.gem.gz GEM 616.66MB afcb148d2b576a260e583ad125b86bd4
C04138G3.tissue.gef GEF 7.88GB 74f3ebd0f1387f9fefa1337b0534c892
C04138G3.raw.gef GEF 1.27GB b9f0c5058f9e3562eed645b862de8f10
C04138G3.report.html HTML 54.75MB 119dd667d308ffd4621cf1e59b031417
C04138G3.visualization.tar.gz TAR 5.35GB e0be0dd93d34481f5312e1d04fd68439
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