|
| Status |
Public on Mar 27, 2023 |
| Title |
cortex and corpus callosum, WT2 |
| Sample type |
SRA |
| |
|
| Source name |
cortex and corpus callosum
|
| Organism |
Mus musculus |
| Characteristics |
tissue: cortex and corpus callosum
strain: C57BL/6J
age: Eight-week-old
Sex: male
genotype: WT
treatment: regular chow
|
| Treatment protocol |
Eight-week-old male wild-type (WT) mice were fed with 0.2% CPZ or regular chow and three experimental groups were set up: a) demyelination (5-week CPZ treatment); b) remyelination (5-week CPZ treatment, followed by 2-week regular chow); c) control (regular chow throughout the time course)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Flash frozen brain tissues were homogenized in a Dounce homogenizer in Lysis Buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, and 0.025% NP-40), and incubated on ice for 15 min. The suspension was filtered through a 30-μm filter to remove debris and pelleted at 500g for 5 min at 4 oC. Nuclei were washed and filtered twice with Nuclei Wash buffer (1% BSA in PBS with 0.2 U μl–1 RNasin (Promega)). Nuclei pellets were resuspended in 500 μl nuclei wash buffer and 900 µl 1.8 M sucrose. This 1,400 μl mixture was carefully layered on top of 500 μl 1.8 M sucrose and centrifuged at 13,000g for 45 min at 4 oC to separate the nuclei from myelin debris. The nuclei pellet was resuspended in nuclei wash buffer at 1,000 nuclei μl–1 and filtered through a 40-μm FlowMi Cell Strainer.
Chromium Single Cell 5' Reagent Kit (v1)
single nucleus RNA sequencing
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Cell Ranger Software Suite (v3.0.2) from 10X Genomics was used for sample demultiplexing, barcode processing, and single-cell counting. Cell Ranger count was used to align samples to the reference genome GRCm38 (mm10), quantify reads, and filter reads and barcodes. Downstream analysis was performed using the Seurat package.
Assembly: To include Clec7a gene, we built a custom reference genome by adding Clec7a cDNA to the pre-built mouse reference genome (mm10)
Supplementary files format and content: raw aligned barcode and feature count matrices from cellranger count (.h5)
|
| |
|
| Submission date |
May 24, 2022 |
| Last update date |
Mar 27, 2023 |
| Contact name |
Yingyue Zhou |
| E-mail(s) |
[email protected]
|
| Organization name |
Washington University in St. Louis
|
| Department |
Pathology and Immunology
|
| Lab |
Marco Colonna
|
| Street address |
425 South Euclid Ave, 8107, 8th floor BJCIH,, Pathology and Immunology
|
| City |
Saint Louis |
| State/province |
Missouri |
| ZIP/Postal code |
63110 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE204755 |
Transcriptomic atlas and interaction networks of brain cells in mouse CNS demyelination and remyelination [B6] |
| GSE204770 |
Transcriptomic atlas and interaction networks of brain cells in mouse CNS demyelination and remyelination |
|
| Relations |
| BioSample |
SAMN28647729 |
| SRA |
SRX15446122 |
