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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Oct 05, 2023 |
| Title |
cortex, homogenate, rep4 |
| Sample type |
SRA |
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| Source name |
cerebral cortex
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| Organism |
Mus musculus |
| Characteristics |
tissue: cerebral cortex
cell type: cortical cell
genotype: WT
treatment: homogenate
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| 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.
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| Growth protocol |
The transgenic mice, including SMACreER:Ai14 and hGFAPCreER:Ai14, were bred, then for cell sorting.
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| 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.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
cortex4
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| 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
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| Submission date |
Sep 09, 2022 |
| Last update date |
Oct 05, 2023 |
| Contact name |
Dong-Dong Zhang |
| E-mail(s) |
2008010556zdd@gmail.com
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| Phone |
08613051063166
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| Organization name |
Fudan University
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| Street address |
130 Dong'an Road
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| City |
Shanghai |
| State/province |
Shanghai |
| ZIP/Postal code |
200032 |
| Country |
China |
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| Platform ID |
GPL19057 |
| Series (1) |
| GSE213026 |
Synaptic-like transmission between neural axons and arterial smooth muscle cells drives cerebral neurovascular coupling |
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| Relations |
| BioSample |
SAMN30755325 |
| SRA |
SRX17506677 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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