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| Status |
Public on Nov 19, 2022 |
| Title |
IVH-1d-1-50 |
| Sample type |
SRA |
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| Source name |
Brain
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| Organism |
Mus musculus |
| Characteristics |
tissue: Brain
strain: C57/BL6
treatment: The needle-puncture group with blood injection at 1st day
time: Day 1
Sex: male
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| Treatment protocol |
These mice were housed in a temperature-controlled room under specific-pathogen-free conditions and a standard 12-h light/dark cycle, with ad libitum access to food and water.
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| Growth protocol |
Five wild-type C57/BL6 mice (weighing 25±5 g, 8 weeks old, Experimental Animal Center of Third Military Medical University, Chongqing, China) were used in this study.
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| Extracted molecule |
total RNA |
| Extraction protocol |
RT-PCR,TRANSCRIPTOMIC.Read length for mate1(bp) is 150 and read length for mate2(bp) is 150.Sequencing was performed with a Novaseq PE150 platform according to the manufacturer’s instructions (Illumina) at an average depth of 300 million read-pairs per sample.
We collected wild-type C57/BL6 mouse brains, which were classified into the no-surgery group (control), the needle-puncture group without blood injection (sham), and the needle-puncture group with blood injection at 1st, 3rd and 7th day. Then, these brains were frozen on dry ice in OCT.Frozen brains were then sectioned coronally at 10 μm on a cryostat and mounted on 10x Genomics Visium spatial transcriptome slides. The tissue locations of the library patches started from the emergence of the lateral ventricle with 20 μm intervals and a 10 μm margin of error.
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| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
We use in-house script to perform basic statistics of raw data, and evaluate the data quality and GC content along the sequencing cycles.
Raw FASTQ files and histology images were processed by sample with the Space Ranger (version spaceranger-1.2.0, 10X Genomics) software with default parameters.
The filtered gene-spots matrix and the fiducial-aligned low-resolution image was used for down-streaming data analyses.
Assembly: mm10
Supplementary files format and content: The tar archive includes:
filtered_feature_bc_matrix
raw_feature_bc_matrix
spatial
filtered_feature_bc_matrix.h5
sample.web_summary.html
molecule_info.h5
raw_feature_bc_matrix.h5
Library strategy: specify
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| Submission date |
Sep 28, 2022 |
| Last update date |
Nov 20, 2022 |
| Contact name |
Jiayidaer Badai |
| E-mail(s) |
2019323040006@stu.scu.edu.cn
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| Organization name |
Sichuan University
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| Street address |
No. 24, South Section 1, First Ring Road, Wuhou District
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| City |
Chengdu |
| ZIP/Postal code |
610065 |
| Country |
China |
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| Platform ID |
GPL24247 |
| Series (1) |
| GSE214349 |
Discovering Haematoma-Stimulated Circuits for Secondary Brain Injury after Intraventricular Haemorrhage by Spatial Transcriptome Analysis |
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| Supplementary file |
Size |
Download |
File type/resource |
| GSM6604483_IVH_1d_1_50.tar.gz |
376.7 Mb |
(ftp)(http) |
TAR |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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