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Spatial Gene Expression of Rat embryo Formalin-fixed Paraffin Embedded Tissue

Stereo-seq N FFPE V1.1, software version: SAW 8.2 & StereoMap 4.2
Stereo-seq OMNI Solution
Rat Embryo Demo Data
Chip SN: Y40320NA
Sample information
Kit information
Experiment information
Sequencing
Analysis result
Input file & Output and supplemental files
Data Details
Sample information
Species : 

Rat (Strain: SD; Age: E12)

Tissue : 

Embryo

Embedding method : 
Formalin-fixed paraffin embedded
DV 200 > 
70%
Kit information
Product : 
Stereo-seq OMNI FFPE
Kit version : 
Stereo-seq N FFPE V1.1
Chip size : 
1 cm × 1 cm
Experiment information
Section thickness : 
5 μm
Staining type : 
ssDNA staining    
Permeabilization time : 
30 min
Sequencing
Total reads : 

2,853,413,387

Sequencer : 
DNBSEQ-G400RS
Analysis result
STOmics Rat embryo Intestine Demo Data Clustering map STOmics Rat embryo Intestine Demo Data Clustering map STOmics Rat embryo Intestine Demo Data Clustering map
Clustering map
  • Analyze Software Version : SAW V8.2, StereoMap V4.2
  • Bin200 Median MID : 22,340

  • Bin200 Median Gene Type : 7,164

  • Bin20 Median MID : 228
  • Bin20 Median Gene Type : 192
  • Cell Bin Gene Type : 173
  • Cell Bin MID : 207
  • Sequencing Saturation : 78.0%

  • Fraction MID in Spots Under Tissue : 87.90%

  • This demo dataset is based on standard SAW results with manual tissue correction and manual Cellbin annotation.


Explore View report
Input files Output and supplemental files
Select All
 Input files Format Size md5sum
Download Selected
Y40320NA_input_command_download
Y40320NA.barcodeToPos.h5 H5 3.17GB a869a4ca1db5d3f1593855b1611a7dcc
Y40320NA_manual_tissue_seg.tif TIFF 1.19MB aa97f10db3e4f9249c02a2de4cccb3cb
Y40320NA_SC_20251106_125232_4.2.0.tar.gz TAR 309.62MB 97be8e6d5e04fec7a2b029debbf83827
V350383172_L01_read_1.fq.gz FQ 12.11GB ee77c495971de152cdf254e2ef3895f5
V350383172_L01_read_2.fq.gz FQ 14.95GB 363069836ed6029dba282d42375d3472
V350383172_L02_read_1.fq.gz FQ 12.01GB cccdfabb31e7b7a473511835b2af4088
V350383172_L02_read_2.fq.gz FQ 14.92GB 9003693e480a60f9dc4d8bb3e7dbca53
V350383172_L03_read_1.fq.gz FQ 11.90GB 50c4884b70a5a90eda02dcc44e57bace
V350383172_L03_read_2.fq.gz FQ 14.76GB ce99d0910618f13c9cd18c0eac9749a9
V350383172_L04_read_1.fq.gz FQ 11.90GB e1735c3817511c7423894604d0b9f682
V350383172_L04_read_2.fq.gz FQ 14.75GB 5a1f7875668a6f21e47e5cd70bfcae01
V350383259_L01_read_1.fq.gz FQ 11.71GB 97165df6e17ee3362047f7bff46b6feb
V350383259_L01_read_2.fq.gz FQ 13.62GB 6add613fce781d6c2dd90ee8a0460d43
V350383259_L02_read_1.fq.gz FQ 11.63GB e0068dba8d23f1346f899f19817ec949
V350383259_L02_read_2.fq.gz FQ 13.51GB a73c45261c647f6e4021ac762ddd1c83
Select All
 Output and supplemental files Format Size md5sum
Download Selected
Y40320NA_output_command_download
Y40320NA.adjusted.cellbin.gef GEF 1.58GB 7fc4aa5a65614d52ac00b6e2474f1777
Y40320NA.cellbin.gef GEF 826.07MB abf24e68c28cc15bdef0dc9140d189c5
Y40320NA.raw.gef GEF 1.55GB b487d308c27f41ff6ec47b2e2a617be3
Y40320NA.report.html HTML 109.95MB 3bb8d598fa09e3526e5858b834de6b0d
Y40320NA_ssDNA_regist.tif TIFF 224.57MB 8a8660a026f6a26c866e51d055471a9c
Y40320NA.tissue.gef GEF 8.70GB 4ee6efe2797244d35c27098aa2958d18
Y40320NA.visualization.tar.gz TAR 7.52GB a9aee9876723f27a823eab28e40fb6bd
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