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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 OMNl Solution
Mouse Brain Demo Data
Chip SN: C04144D5
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 : 
ssDNA staining
Permeabilization time : 
30 min
Sequencing
Total reads : 
2,973,434,937
Sequencer : 
DNBSEQ-G400RS, DNBSEQ-T7RS
Analysis result
Clustering map
  • Analyze Software Version : SAW V8.1, StereoMap V4.1
  • Bin200 Median MID : 44,831
  • Bin200 Median Gene Type : 6,087
  • Cell Bin Gene Type : 186
  • Cell Bin MID : 442
  • Sequencing Saturation : 73.10%
  • Fraction MID in Spots Under Tissue : 92.70%
Explore View report
Input files Output and supplemental files
Select All
 Input files Format Size md5sum
Download Selected
C04144D5_input_command_download TXT 4.27KB f7a7b30e4a45d0dd6689e1c93682bd8f
V350265067_L03_read_1.fq.gz FQ 8.87GB d6125b2370590982163816002a88334f
V350265067_L03_read_2.fq.gz FQ 18.04GB d2aab38a968d47311388e71fed29beca
E250018411_L01_6_1.fq.gz FQ 17.38GB b3be1d6f17493c2adcc85880838d9be0
E250018411_L01_6_2.fq.gz FQ 31.41GB 0d7e038127cbc9f91c880f3248206424
E250018411_L01_5_1.fq.gz FQ 15.69GB c4557a6688803817dd2dfe841fbf2de7
E250018411_L01_5_2.fq.gz FQ 28.54GB 3ec1a3e15f120ff5a1693127569b8f3b
E250018259_L01_6_1.fq.gz FQ 17.50GB dff188d32ef7fedd481d277abc0dbd18
E250018259_L01_6_2.fq.gz FQ 31.90GB ea98d33b2cebc7575355c8792a5326f4
E250018259_L01_5_1.fq.gz FQ 15.83GB d3ca14970632ac2733e052b7277bc9ef
E250018259_L01_5_2.fq.gz FQ 29.02GB 1c83ab5be8dcf3f54245c5e27526485f
C04144D5_SC_20240613_104803_4.0.0.tar.gz TAR 195.15MB 4a20efc8870433433adb1565d3a7f0a8
C04144D5.barcodeToPos.h5 H5 3.17GB da2e952f6a75d94f0fbfe964ff06835a
Select All
 Output and supplemental files Format Size md5sum
Download Selected
C04144D5_output_command_download TXT 2.84KB 46ae0ba87f8f7625dcde9ce0afaeae35
C04144D5.visualization.tar.gz TAR 4.67GB 53f51c70ec5345b12cec9105d088eef1
C04144D5.report.html HTML 49.36MB d50a26e59dea6180721c2f3a51e30636
C04144D5.raw.gef GEF 1.55GB bea87c3557e5e0f88f7ccfb228540f6a
C04144D5.tissue.gef GEF 8.70GB 10a91141ad8d8cde08c7e7bac7fbef84
C04144D5.tissue.gem.gz GEM 700.25MB 6e30d57127d6e78f50ca85c948a0e7fe
C04144D5.cellbin.gef GEF 375.57MB e3fe99113b38ff1f754b6cea1abdf9e4
C04144D5.adjusted.cellbin.gef GEF 796.53MB 82e5362af62937d7ca8a87b254cf29ec
C04144D5_ssDNA_regist.tif TIFF 158.84MB 6e1612b821c6586e0a225ea13bfcf742
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