|
| Status |
Public on Apr 15, 2024 |
| Title |
Chat-cre; CAG-Sun1/sfGFP mice NA |
| Sample type |
SRA |
| |
|
| Source name |
flash frozen nucleus ambiguous of the brainstem
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: flash frozen nucleus ambiguous of the brainstem
age: 10-week-old
Sex: pooled male and female
genotype: Chat-cre; CAG-Sun1/sfGFP
treatment: no treatment
|
| Treatment protocol |
no treatment
|
| Growth protocol |
All Mice used in this experiment are bred in the standard facility of UCSD with approval protocol from IACUC
|
| Extracted molecule |
nuclear RNA |
| Extraction protocol |
Cellular suspensions were loaded on a 10X Genomics Chromium Controller (10x Genomics, Pleasanton, CA) to generate single cell GEMs. cDNA extraction and amilification were excecuted using Chromium Single Cell 3' Reagent Kits (v3 Chemistry, PN-1000075, 10X Genomics) folloing User Guide provided by 10X Genomics.
Single cell RNA-Seq libraries were prepared using GemCode Single Cell 3’ Gel Bead and Library Kit v3 (PN-1000075, 10x Genomics) following User Guide provided by 10X Genomics.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Raw data in fastqs format. UMI count matrix files (h5) from cellranger. Seurat object in R object.
|
| Data processing |
Sequencing was carried out on NovaSeq (Illumina) platform at the Institute for Genomic Medicine, UCSD.
Cell Ranger package (version 3.0.2) was used to align the raw reads onto the mouse reference genome (GRCm38) with default parameters and generate the feature-barcode matrix.
R package Seurat (version 4.0) was used to perform data quality control, normalization, principal components analysis and uniform manifold approximation and projection (UMAP method).
Cells with more than 200 unique feature counts were considered high quality cells and used for further analysis.
We firstly used SCTransform.The dataset was normalized, scaled, and then analyzed for variable genes using Seurat’s NormalizeData, ScaleData, and FindVariableFeatures functions, respectively. A total of 2,000 top variable features were identified by function FindVariableFeatures and selected for subsequent principal components analysis.
Top 20 significant components were chosen to conduct cell clustering by using the algorithm of uniform manifold approximation and projection (UMAP) with default settings. The expression level and feature of selected genes were profiled and visualize by R package ggplot2 (version 3.3.2).
Assembly: Genome Reference Consortium Mouse Build 38 patch release 6 (GRCm38.p6)
Supplementary files format and content: Raw data-Reads alignment files in fastqs format. UMI count matrix files (h5) from cellranger. Seurat object in R object (rds).
|
| |
|
| Submission date |
Aug 18, 2022 |
| Last update date |
Apr 15, 2024 |
| Contact name |
Yujuan Su |
| E-mail(s) |
yus018@ucsd.edu
|
| Phone |
18583092532
|
| Organization name |
UCSD
|
| Street address |
9500 Gilman Dr. MC0766 CMME, Room 1087
|
| City |
San Diego |
| State/province |
CALIFORNIA |
| ZIP/Postal code |
92093 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE211538 |
Brainstem Dbh+ Neurons Control Chronic Allergen-Induced Airway Hyperreactivity |
|
| Relations |
| BioSample |
SAMN30385643 |
| SRA |
SRX17133371 |
