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Spatial Gene Expression of Rat Brain Fresh Frozen Tissue

Stereo-seq T FF V1.3, software version: SAW 8.1 & StereoMap 4.1
Stereo-seq Transcriptomics Solution
Rat Brain Demo Data
Chip SN: D04499F5G6
Sample information
Kit information
Experiment information
Sequencing
Analysis result
Input file & Output and supplemental files
Data Details
Sample information
Species : 
Rat (Strain: SD; Sex: Male; Age: 6-8 week)
Tissue : 
Brain
Embedding method : 
Fresh frozen
RIN value : 
8.2
Kit information
Product : 
Stereo-seq FF
Kit version : 
Stereo-seq T FF V1.3
Chip size : 
2 cm × 2 cm
Experiment information
Section thickness : 
10 μm
Staining type : 
ssDNA staining
Permeabilization time : 
14 min
Sequencing
Total reads : 
4,563,251,639
Sequencer : 
DNBSEQ-T7RS
Analysis result
Clustering map
  • Analyze Software Version : SAW 8.1, StereoMap 4.1
  • Bin200 Median MID : 50,043

  • Bin200 Median Gene Type : 10,099

  • Bin20 Median MID : 439

  • Bin20 Median Gene Type : 368

  • Cell Bin Gene Type : 601
  • Cell Bin MID : 751
  • Sequencing Saturation : 47.7%
  • Fraction MID in Spots Under Tissue : 83.57%

Explore View report
Input files Output and supplemental files
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 Input files Format Size md5sum
Download Selected
E250087856_L01_4_2.fq.gz FQ 141.49GB 8666a0b6fbbca40bdfe7258087406a14
E250087856_L01_4_1.fq.gz FQ 64.19GB cdf23cbf060e9bf03c7c982141e26b05
E250087856_L01_3_2.fq.gz FQ 73.32GB 4eef7586113fffd67e716b9e55152464
E250087856_L01_3_1.fq.gz FQ 33.64GB 3a6b6b4052b5d1bbd047d4398d7aa516
E250087856_L01_2_2.fq.gz FQ 65.95GB f8914584f9c161b19df2e6fd3cbc67ed
E250087856_L01_2_1.fq.gz FQ 30.01GB 7f456956c01728ed20ec887b33a524f1
E250087856_L01_1_2.fq.gz FQ 71.48GB 19a44e5927058eeb4bccab85c3aacfbe
E250087856_L01_1_1.fq.gz FQ 32.52GB 5626b7a3887ff32c9cce9f4200df531a
D04499F5G6_SC_20250605_182007_4.1.2.tar.gz TAR 541.04MB 83b7d9464f5faa56b0c43887786367cc
D04499F5G6.barcodeToPos.h5 H5 9.32GB 6b951ae8bd8be79fb8ff1c48bcd47b3b
D04499F5G6_input_command_download TXT
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 Output and supplemental files Format Size md5sum
Download Selected
D04499F5G6.visualization.tar.gz TAR 20.12GB 3d2404e75c89a6aada30748e28555c83
D04499F5G6.tissue.gem.gz GEM 2.45GB 3710b9d34922531b29492d41948070c9
D04499F5G6.tissue.gef GEF 35.26GB 9f8c81ddffd529635f3ed4fe99d044ac
D04499F5G6_ssDNA_tissue_cut.tif TIFF 2.97MB f3ec810c10c5606abf99e4a488234b6e
D04499F5G6_ssDNA_regist.tif TIFF 453.45MB 4c65252ed8d31804b232dda25f1575a5
D04499F5G6_ssDNA_mask.tif TIFF 16.19MB 3abfaf2e12433dff915a64ed93ef902b
D04499F5G6_ssDNA_mask_edm_dis_10.tif TIFF 23.80MB 2d28daf8b557f7d16a9a2ae28ce12ca2
D04499F5G6.report.html HTML 91.23MB 0dfd347550b14118a5d843265fdf3df3
D04499F5G6.raw.gef GEF 5.83GB 7d28b79183a52c158c5d2b4b52f0d720
D04499F5G6.cellbin.gef GEF 1.89GB ec3d61be1ea67b3c500ddf3bf3554f40
D04499F5G6.adjusted.cellbin.gef GEF 3.95GB 66ace049c0d31b990c270d341b1d3fa5
D04499F5G6_output_command_download TXT
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