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Spatial Gene Expression of Mouse Embryo Fresh Frozen Tissue

Stereo-seq T FF V1.3, software version: SAW 8.1 & StereoMap 4.1
Stereo-seq Large Chip Designs
The STOmics database will undergo scheduled maintenance from June 17 to July 1, 2025. During this period, the online visualization links may be temporarily unavailable. We apologize for any inconvenience caused.
Mouse Embryo Demo Data
Chip SN: D05103C4D4
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: female; Age: E18.5)

Tissue : 

Embryo

Embedding method : 
Fresh frozen
RIN value : 
8.4
Kit information
Product : 
Stereo-seq FF
Kit version : 
Stereo-seq T FF V1.3
Chip size : 
1 cm × 2 cm
Experiment information
Section thickness : 
10 μm
Staining type : 
H&E staining    
Permeabilization time : 
12 min
Sequencing
Total reads : 
4,122,777,778
Sequencer : 
DNBSEQ-T7RS
Analysis result
STOmics Mouse Embryo Demo Data Clustering map STOmics Mouse Embryo Demo Data Clustering map STOmics Mouse Embryo Demo Data Clustering map
Clustering map
  • Analyze Software Version : SAW V8.1, StereoMap V4.1
  • Bin200 Median MID : 82,562

  • Bin200 Median Gene Type : 10,952

  • Bin20 Median MID : 832
  • Bin20 Median Gene Type : 593
  • Cell Bin Gene Type : 433
  • Cell Bin MID : 569
  • Sequencing Saturation : 13.20%

  • Fraction MID in Spots Under Tissue : 88.23%

  • The tissue segmentation was manually corrected, and the cell segmentation was perfomed by third-party algorithm.


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Input files Output and supplemental files
Input files Format Size md5sum
D05103C4D4_input_command_download TXT 6.46KB 365ac576b157a9b7431092ff96074e80
D05103C4D4.barcodeToPos.h5 H5 5.75GB 94a24ccb7d52f18bfe8895f7c45df012
D05103C4D4_SC_20250521_172130_4.1.2.tar.gz TAR 2.24GB 183b621c4194f9105b23d98b6d53b3a3
E250082882_L01_1_1.fq.gz FQ 16.23GB 51e29186cefe921c3416fcc77a0849c9
E250082882_L01_1_2.fq.gz FQ 36.50GB f9f0c63f3999f3de2a538736688676c1
E250082882_L01_2_1.fq.gz FQ 19.70GB b26dc954e78d18446a05a6fe45e96f8e
E250082882_L01_2_2.fq.gz FQ 44.36GB c66f6f42b236695606ad7a1558eed82e
E250082882_L01_3_1.fq.gz FQ 16.08GB 2aee04020265e991180c00509428095a
E250082882_L01_3_2.fq.gz FQ 36.80GB 2822cf9539831cc05bbfad6d5d72ef04
E250082882_L01_4_1.fq.gz FQ 14.53GB 12bee2629c4b5851c807fac452446ca5
E250082882_L01_4_2.fq.gz FQ 33.55GB 117cce6688f8676df5dbe013bd05e891
E250082899_L01_1_1.fq.gz FQ 15.45GB e51f84ea5a1536faaaad499b62199787
E250082899_L01_1_2.fq.gz FQ 33.89GB 23110b639d3c9429e205cfbf89564216
E250082899_L01_2_1.fq.gz FQ 18.93GB f94c6fc8a31fa532f96d0cf6522f1c25
E250082899_L01_2_2.fq.gz FQ 41.51GB dde49bd35e030ab3c41bb5cad2f4a982
E250082899_L01_3_1.fq.gz FQ 15.12GB 0844250e1948067bf188352005103abc
E250082899_L01_3_2.fq.gz FQ 33.79GB 6375ae1ab319d265f99e8bf94ec965c0
E250082899_L01_4_1.fq.gz FQ 13.79GB c168b931b532e5449293e4893f0916dc
E250082899_L01_4_2.fq.gz FQ 31.17GB 2187dbc79014ee7c1c45029083dc2bb8
Output and supplemental files Format Size md5sum
D05103C4D4_output_command_download TXT 2.93KB de0d916eb1f9419b09b16dbe2ac5f3cd
D05103C4D4.visualization.tar.gz TAR 36.67GB 0e9c5fc05b74e4ad3bc14108ba8ce3d2
D05103C4D4.report.html HTML 165.13MB 208410d338f3410e6388c5d3bdaf00fd
D05103C4D4.raw.gef GEF 11.31GB c0430f5e7fca7efa16b8fe7cad632c29
D05103C4D4.tissue.gef GEF 52.87GB a8cf6ac38ff9bf31d677eecdd5a7d0ee
D05103C4D4.tissue.gem.gz GEM 4.64GB 0e5894de60338f79b19df3cfc8a41a48
D05103C4D4.cellbin.gef GEF 4.46GB 1790d1d2071bf1a25a0f25814fbb351f
D05103C4D4.adjusted.cellbin.gef GEF 8.68GB 7d6646728e2ef7a072128adc33e36540
D05103C4D4_HE_regist.tif TIFF 2.10GB 9bbd9f8f227553cd2bc40c16f17813c0
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