Mouse brain C04496D6

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 OMNI Solution

Mouse brain Demo Data

Chip SN: C04496D6

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 :

Formalin-fixed paraffin embedded

RIN value/DV :

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 :

H&E staining

Permeabilization time :

30 min

Sequencing

Total reads :

3,373,360,341

Sequencer :

DNBSEQ-G400RS

Analysis result

Heatmap

Analyze Software Version : SAW V8.1, StereoMap V4.1
Bin200 Median MID : 50,873
Bin200 Median Gene Type : 6,856
Sequencing Saturation : 74.70%
Fraction MID in Spots Under Tissue : 91.37%
Manual tissue segmentation was performed.

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Input files Output and supplemental files

Input files	Format	Size	md5sum
Sequencing FASTQ Files C04496D6_input_command_download	TXT	6.47KB	60568a71ed30fbdae6815bbdb0a80184
V350296375_L04_read_2.fq.gz	FQ	13.07GB	ad39b94c778bf8a74c95db02de37f3b6
V350296375_L04_read_1.fq.gz	FQ	7.30GB	7708b0506cd52c50be6c09a4488cdefb
V350296375_L03_read_2.fq.gz	FQ	14.84GB	1157bec570fa1dabe58ee45ce73b5c60
V350296375_L03_read_1.fq.gz	FQ	8.63GB	04a38e676f4c011699c61ce76aa164f9
V350296375_L02_read_2.fq.gz	FQ	15.40GB	6d39fb0032abfa36eb55ee0b146ea4af
V350296375_L02_read_1.fq.gz	FQ	9.01GB	fadf49d67dac905ab46fd4a4c75693d8
V350296375_L01_read_2.fq.gz	FQ	14.08GB	561cc698cefa84231552d912016f7b27
V350296375_L01_read_1.fq.gz	FQ	7.95GB	5ff72a001c5da18785b89867ddc22618
V350296374_L04_read_2.fq.gz	FQ	17.67GB	c3a0f8500731b55a9aa8c5ab06fb7060
V350296374_L04_read_1.fq.gz	FQ	9.14GB	1cf9b780072e83740755e61586021d26
V350296374_L03_read_2.fq.gz	FQ	17.68GB	df2522a5ce8227d868b2c30f6cedf999
V350296374_L03_read_1.fq.gz	FQ	9.17GB	8b22113d7fb61dd002395c4df35009f8
V350284986_L04_read_2.fq.gz	FQ	17.52GB	dad71011940a36b18e732705918e7535
V350284986_L04_read_1.fq.gz	FQ	9.03GB	6f0397f806c33214196510fbe56cf135
V350284986_L01_read_2.fq.gz	FQ	18.17GB	a35441d2a8b2772e9509eca4a4fafef6
V350284986_L01_read_1.fq.gz	FQ	8.98GB	3a2130caee215fea7fca140966b0e18e
C04496D6_SC_20250306_095555_4.1.2.tar.gz	TAR	1.13GB	2e0409824235a8369fb3175807f8ecfb
C04496D6.barcodeToPos.h5	H5	2.85GB	d91b1fcc651b92e1bbeb83578b232594

Output and supplemental files	Format	Size	md5sum
Sequencing FASTQ Files C04496D6_output_command_download	TXT	2.20KB	3392d25ce4d161bceb9ef93dcdb41404
C04496D6_HE_regist.tif	TIF	912.86MB	d85cfd35cae5478030c7df107f96a0fc
C04496D6.tissue.gem.gz	GEM	827.30MB	b67384f5ab18c845c8c60684a43f8d62
C04496D6.tissue.gef	GEF	9.94GB	49ce65e58c9023fb1361aed08d8f8ecc
C04496D6.raw.gef	GEF	1.81GB	92af3e6f7af7e9717507c9ab73470bcd
C04496D6.report.html	HTML	58.53MB	7f40577f5b39a293c723410c45468b88
C04496D6_visualization.tar.gz	TAR	6.70GB	8f91271b37c9e79ff0c27b362091a069

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