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| Status |
Public on Nov 27, 2024 |
| Title |
Brain pericytes mouse 4 |
| Sample type |
SRA |
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| Source name |
Brain
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| Organism |
Mus musculus |
| Characteristics |
tissue: Brain
cell line: Isolated pericytes
cell type: Pericytes
genotype: Wild-type
batch: 2022-03
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| Extracted molecule |
total RNA |
| Extraction protocol |
Following total RNA extraction, RNA-seq was performed at the NYU Langone Medical Center Genome Technology Center (GTC). Bulk RNA-seq was performed with a NovaSeq 6000 instrument (Illumina). The fastq files were analyzed using the NYU Langone Medical Center’s BigPurple cluster.
SMART-Seq® HT Kit consisting of a one-step cDNA synthesis and amplification, purification and validation of cDNA and library preparation.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
Library name: Sample 4
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| Data processing |
Alignment to was performed using STAR
Assembly: Mouse mm10 genome
Supplementary files format and content: Further analysis was performed with R, using the DESeq package. We filtered out low expressing genes with fewer than 25 summed raw counts across the 10 samples. This reduced the data complexity and decreased the gene count from 39,395 to 20,685. Putative ion channels and transporters (CTP) were extracted from a list of such genes (Github: BillAC/List-of-Channels-and-Transporters).
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| Submission date |
Nov 26, 2024 |
| Last update date |
Nov 27, 2024 |
| Contact name |
William Coetzee |
| E-mail(s) |
[email protected]
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| Organization name |
NYU School of Medicine
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| Department |
Pathology
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| Street address |
550 First Ave
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| City |
New York |
| State/province |
United States |
| ZIP/Postal code |
10514 |
| Country |
USA |
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| Platform ID |
GPL24247 |
| Series (1) |
| GSE282935 |
Bulk RNA-seq of pericytes isolated from mouse brain and heart |
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| Relations |
| BioSample |
SAMN45068041 |
| SRA |
SRX26888296 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
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