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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: C04496D6
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 : 
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 : 
3,373,360,341
Sequencer : 
DNBSEQ-G400RS
Analysis result
Heatmap
  • Analyze Software Version : SAW V8.1, StereoMap V4.1
  • Bin200 Median MID : 50,873
  • Bin200 Median Gene Type : 6,856
  • Sequencing Saturation : 74.70%
  • Fraction MID in Spots Under Tissue : 91.37%
  • Manual tissue segmentation was performed.

Explore View report
Input files Output and supplemental files
Select All
 Input files Format Size md5sum
Download Selected
C04496D6_input_command_download TXT 6.47KB 60568a71ed30fbdae6815bbdb0a80184
V350296375_L04_read_1.fq.gz FQ 7.30GB 7708b0506cd52c50be6c09a4488cdefb
V350296375_L04_read_2.fq.gz FQ 13.07GB ad39b94c778bf8a74c95db02de37f3b6
V350296375_L03_read_1.fq.gz FQ 8.63GB 04a38e676f4c011699c61ce76aa164f9
V350296375_L03_read_2.fq.gz FQ 14.84GB 1157bec570fa1dabe58ee45ce73b5c60
V350296375_L02_read_1.fq.gz FQ 9.01GB fadf49d67dac905ab46fd4a4c75693d8
V350296375_L02_read_2.fq.gz FQ 15.40GB 6d39fb0032abfa36eb55ee0b146ea4af
V350296375_L01_read_1.fq.gz FQ 7.95GB 5ff72a001c5da18785b89867ddc22618
V350296375_L01_read_2.fq.gz FQ 14.08GB 561cc698cefa84231552d912016f7b27
V350296374_L04_read_1.fq.gz FQ 9.14GB 1cf9b780072e83740755e61586021d26
V350296374_L04_read_2.fq.gz FQ 17.67GB c3a0f8500731b55a9aa8c5ab06fb7060
V350296374_L03_read_1.fq.gz FQ 9.17GB 8b22113d7fb61dd002395c4df35009f8
V350296374_L03_read_2.fq.gz FQ 17.68GB df2522a5ce8227d868b2c30f6cedf999
V350284986_L04_read_1.fq.gz FQ 9.03GB 6f0397f806c33214196510fbe56cf135
V350284986_L04_read_2.fq.gz FQ 17.52GB dad71011940a36b18e732705918e7535
V350284986_L01_read_2.fq.gz FQ 18.17GB a35441d2a8b2772e9509eca4a4fafef6
V350284986_L01_read_1.fq.gz FQ 8.98GB 3a2130caee215fea7fca140966b0e18e
C04496D6_SC_20250306_095555_4.1.2.tar.gz TAR 1.13GB 2e0409824235a8369fb3175807f8ecfb
C04496D6.barcodeToPos.h5 H5 2.85GB d91b1fcc651b92e1bbeb83578b232594
Select All
 Output and supplemental files Format Size md5sum
Download Selected
C04496D6_output_command_download TXT 2.20KB 3392d25ce4d161bceb9ef93dcdb41404
C04496D6_HE_regist.tif TIF 912.86MB d85cfd35cae5478030c7df107f96a0fc
C04496D6.tissue.gem.gz GEM 827.30MB b67384f5ab18c845c8c60684a43f8d62
C04496D6.tissue.gef GEF 9.94GB 49ce65e58c9023fb1361aed08d8f8ecc
C04496D6.raw.gef GEF 1.81GB 92af3e6f7af7e9717507c9ab73470bcd
C04496D6.report.html HTML 58.53MB 7f40577f5b39a293c723410c45468b88
C04496D6_visualization.tar.gz TAR 6.70GB 8f91271b37c9e79ff0c27b362091a069
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