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Sample GSM6475220 Query DataSets for GSM6475220
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
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
BioSample SAMN30385643
SRA SRX17133371

Supplementary file Size Download File type/resource
GSM6475220_Updated_NA.rds.gz 44.3 Mb (ftp)(http) RDS
GSM6475220_filtered_feature_bc_matrix.h5 42.5 Mb (ftp)(http) H5
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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