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Spatial Gene Expression of Mouse Brain Fresh Frozen Tissue

Stereo-seq T FF V1.3, software version: SAW 8.1 & StereoMap 4.0
Stereo-seq Transcriptomics Solution
Mouse brain Demo Data
Chip SN: C03937C4
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 : 
Fresh frozen
RIN value : 
8
Kit information
Product : 
Stereo-seq FF
Kit version : 
Stereo-seq T FF V1.3
Chip size : 
1 cm × 1 cm
Experiment information
Section thickness : 
10 μm
Staining type : 
DAPI + mIF staining
Permeabilization time : 
12 min
Sequencing
Total reads : 
1,747,834,723
Sequencer : 
DNBSEQ-G400RS
Analysis result
Clustering map
  • Analyze Software Version : SAW V8.1, StereoMap V4.0
  • Bin200 Median MID : 44,309
  • Bin200 Median Gene Type : 8,482
  • Cell Bin Gene Type : 732
  • Cell Bin MID : 1,133
  • Sequencing Saturation : 79.3%
  • Fraction MID in Spots Under Tissue : 88.81%

  • NeuN and SMI32 images were manually calibrated with the DAPI image.



Explore View report >
Input files Output and supplemental files
Input files Format Size md5sum
C03937C4_input_command_download TXT 3.40KB e2c4ab611528d75de73f5596053a5e7e
V350306380_L04_read_1.fq.gz FQ 10.83GB ca8cc229cca54428dffdcb2d66e44b07
V350306380_L04_read_2.fq.gz FQ 14.52GB 636461b4c6f90606dfa7a39f3fef7bf6
V350306380_L03_read_1.fq.gz FQ 10.89GB 7ebccecbf08f540eb127ac30f9428311
V350306380_L03_read_2.fq.gz FQ 14.58GB b9ee2deef2613429e0ea86452ba72e3f
V350306380_L02_read_1.fq.gz FQ 10.95GB 06a29779ad728488aceef7545747fae1
V350306380_L02_read_2.fq.gz FQ 14.66GB 3bd605befa4eff332ca61523a426bdc7
V350306380_L01_read_1.fq.gz FQ 11.02GB 3dbc3813ce0d24f7b31752bf2ef61abb
V350306380_L01_read_2.fq.gz FQ 14.75GB 43945d203e861186ddbf415b72d3eb31
C03937C4_SC_20250317_200459_4.0.1.tar.gz TAR 2.87GB df363a89bbb7d723c8e1f1d311e79a2f
C03937C4.barcodeToPos.h5 H5 3.18GB 8a6bd0056799dc8e041875984b5fb528
Output and supplemental files Format Size md5sum
C03937C4_output_command_download TXT 3.18KB e89b8d2596defa455b373173458e9f45
C03937C4.tif.tar.gz TAR 1.45GB fce490b4e2240b2da4a717d349acaae7
C03937C4_DAPI_regist.tif TIFF 168.40MB 8747ffb4ca33b0c89e7fe8f04ebf6209
C03937C4.adjusted.cellbin.gef GEF 908.96MB 2430cec85666c433abcfb113b5730d3a
C03937C4.cellbin.gef GEF 424.55MB faf6965d68aee2a1e46919f8be666455
C03937C4.tissue.gem.gz GEM 570.04MB 21a1459a3852974f61f889c13480825d
C03937C4.tissue.gef GEF 8.24GB dc63cbe953c7e459c82ac800886b6b64
C03937C4.raw.gef GEF 1.24GB 17c5e101777e164cc479803cc1c0945f
C03937C4.report.html HTML 50.81MB b534e2a6407e12ad6ce7dea9e3a23fd9
C03937C4.visualization.tar.gz TAR 7.11GB 6b93bcdfdf570ec3816a3787dc4ded82
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