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Sample GSM6568826 Query DataSets for GSM6568826
Status Public on Oct 05, 2023
Title cortex, homogenate, rep1
Sample type SRA
 
Source name cerebral cortex
Organism Mus musculus
Characteristics tissue: cerebral cortex
cell type: cortical cell
genotype: WT
treatment: homogenate
Treatment protocol Using the Ai14 reporter mice, the tdtomato positive cells labeling aSMCs or astrocytes were acquired by fluorescence-activated cell sorting (FACS), then for RNA extraction.
Growth protocol The transgenic mice, including SMACreER:Ai14 and hGFAPCreER:Ai14, were bred, then for cell sorting.
Extracted molecule total RNA
Extraction protocol RNA was harvested using RNeasy plus mini kit (Qiagen). Total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Ovation RNA-Seq system V2 and Ovation Ultralow system V2 (NuGEN) following manufacturer's protocols.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Description cortex1
Data processing Ubuntu terminal environment in minutes with Windows Subsystem for Linux (WSL), v 20.04.4. Conda for managing and deploying applications, environments and packages in RNA-Seq, v 4.14.0.
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trim-galore, v 0.6.7 (parameter: --quality score 25, --cores 4, --phred 33, --length 35, --stringency 3).
Trimmed sequence reads were processed to Quality control using FastQC, v 0.11.9 and MultiQC, v 1.13.
Trimmed sequence reads were mapped to GrCM38 using Salmon index, and then were genetic quantified using Salmon quant, v 1.4.0.
Read count extraction and matrix were performed using tximport package in R, v 4.1.0.
Assembly: Grcm38
Supplementary files format and content: tab-delimited text files include counts values for each Sample
 
Submission date Sep 09, 2022
Last update date Oct 05, 2023
Contact name Dong-Dong Zhang
E-mail(s) 2008010556zdd@gmail.com
Phone 08613051063166
Organization name Fudan University
Street address 130 Dong'an Road
City Shanghai
State/province Shanghai
ZIP/Postal code 200032
Country China
 
Platform ID GPL19057
Series (1)
GSE213026 Synaptic-like transmission between neural axons and arterial smooth muscle cells drives cerebral neurovascular coupling
Relations
BioSample SAMN30755328
SRA SRX17506674

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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