|
| Status |
Public on Jul 20, 2024 |
| Title |
PVT-Second |
| Sample type |
SRA |
| |
|
| Source name |
brain-PVT area
|
| Organism |
Mus musculus |
| Characteristics |
tissue: brain-PVT area
cell line: fresh tissue
cell type: all cells in the brain-PVT area
strain: C57BL/6
treatment: no treatment
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Mice were anaesthetized with 2% isoflurane, and then the brains were rapidly removed. The brain was frozen using a freezing microtome (CM1850; Leica, Buffalo Grove, IL, USA) and then cut into slices (~300 μm). The PVT tissues were taken quickly and stored in liquid nitrogen.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
The single cell suspension was loaded into Chromium microfluidic chips with 30 (v2 or v3, depends on project) chemistry and barcoded with a 10 Chromium Controller (10X Genomics).
RNA from the barcoded cells was subsequently reverse-transcribed and sequencing libraries constructed with reagents from a Chromium Single Cell 30 v2 (v2 or v3, depends on project) reagent kit (10X Genomics) according to the manufacturer’s instructions.
Sequencing was performed with Illumina (HiSeq 2000 or NovaSeq) according to the manufacturer’s instructions (Illumina).
Raw reads were demultiplexed and mapped to the reference genome by a 10X Genomics Cell Ranger pipeline using the default parameters.
Assembly: mm8
Supplementary files format and content: Tab-separated values files and matrix files
|
| |
|
| Submission date |
Aug 08, 2023 |
| Last update date |
Jul 20, 2024 |
| Contact name |
Cheng Zhou |
| E-mail(s) |
zhouc1985@gmail.com
|
| Organization name |
West China Hospital of Sichuan University
|
| Street address |
No District, Chengdu, Sichuan Province. 37 Guoxue Lane, Wuhou
|
| City |
Chengdu |
| State/province |
Sichuan |
| ZIP/Postal code |
610000 |
| Country |
China |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE240388 |
Astrocytes modulate a specific paraventricular thalamus-prefrontal cortex projection to enhance consciousness recovery from sevoflurane anesthesia in mice |
|
| Relations |
| BioSample |
SAMN36892640 |
| SRA |
SRX21301797 |
