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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 4.1
Mouse brain Demo Data
Chip SN: C04042E2
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: 8-9 week)
Tissue
Whole brain
Embedding method
Fresh frozen
RIN value/DV
7
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
ssDNA staining
Permeabilization time
12 min
Sequencing
Total reads
1,763,421,296
Sequencer
DNBSEQ-G400RS; DNBSEQ-T7RS
Analysis result
Clustering map
  • Analyze Software Version : SAW V8.1, StereoMap V4.1
  • Bin200 Median MID : 51,538
  • Bin200 Median Gene Type : 11,790
  • Cell Bin Gene Type : 916
  • Cell Bin MID : 1,698
  • Sequencing Saturation : 73.5%
  • Fraction MID in Spots Under Tissue : 81.46%

Input files Output and supplemental files
Input files Format Size md5sum
Sequencing FASTQ Files C04042E2_input_command_download TXT 2.8KB 01dd69900ab6144b0c265a277b91def2
S_E250018404_L01_read_2.fq.gz FQ 34.47GB f752dcdc9091ea1e1e0d50331570ee77
S_E250018404_L01_read_1.fq.gz FQ 33.40GB cd40f3533f39c23f2f4145fd18c775e6
V350272816_L02_read_2.fq.gz FQ 13.34GB 589c9ac6642f9b91f10eee70e7ef99e4
V350272816_L02_read_1.fq.gz FQ 10.37GB 3a6dcf0c4459d13111eda599d3fe6cdf
V350272816_L01_read_2.fq.gz FQ 13.95GB 5e5b39dacf86a20742b0c4190fbe232f
C04042E2_SC_20240925_144329_4.1.0.tar.gz TAR 168.88MB c3adb92aeba00137c782e75f4c818065
V350272816_L01_read_1.fq.gz FQ 10.77GB 23760aa784c929cdab7129d024f25a0c
C04042E2.barcodeToPos.h5 H5 3.03GB 62c4052da95604939ae2aff66d0cc94b
Output and supplemental files Format Size md5sum
Sequencing FASTQ Files C04042E2_output_command_download TXT 2.84KB 64cd94616e0abfc8f61b693fa9081e43
C04042E2_ssDNA_regist.tif TIFF 152.78MB 0791314d424a076dd6e274e6a2a0d800
C04042E2.adjusted.cellbin.gef GEF 175GB 05b13960715d4582d4afba343e5747ea
C04042E2.cellbin.gef GEF 837.75MB fa1bc6552cac5e5c4b7bfa7cb44bbd59
C04042E2.tissue.gem.gz GEM 1.17GB de1691ac754fb1aaa72e3b16f56ed12a
C04042E2.tissue.gef GEF 14.92GB dedb43bfbde09961028bc2ac93766951
C04042E2.raw.gef GEF 2.54GB 2c91c7f0cd06eff13502fa0883a4acad
C04042E2.report.tar.gz TAR (HTML) 28.49MB acd98099ce71a1581253e64a7b06b18f
C04042E2.visualization.tar.gz TAR 8.85GB 7b379ce3f05f6da3f9cbd2aedd524d18
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