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Status |
Public on Oct 22, 2019 |
Title |
10A2-1 |
Sample type |
SRA |
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Source name |
hCMEC/D3 cell lines
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Organism |
Homo sapiens |
Characteristics |
tissue: brain vascular cell type: temporal lobe microvessels agent: single atorvastatin
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Treatment protocol |
Hematoma was purchased from CSDH patients. The supernatant of the hematoma was collected after centrifugation at 3000 rpm for 15 min and stored at -80 ℃. Subsequently, PBS, atorvastatin, dexamethasone, or a combination of atorvastatin and dexamethasone was added to the hematoma followed by co-culture with hCMEC/D3 for 1 h. The stimulated group of cells was transferred to normal medium containing no drugs.
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Growth protocol |
hCMEC/D3 was obtained from Sigma-Aldrich , cultured in endothelial cell medium(ECM), and grown on 0.1% collagen type I-coated coverslips until a tight monolayer was formed. Medium was changed every other day.
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Extracted molecule |
total RNA |
Extraction protocol |
The treated cells were removed, washing three times on dry ice, and RNA was harvested using Trizol reagent RNA libraries were prepared for sequencing using standard Illumina protocols, NEBNext® Ultra™ RNA Library Prep Kit for Illumina
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina NovaSeq 6000 |
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Description |
10A2-1
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Data processing |
Illumina Casava1.7 software used for basecalling. Filter:1) Trim Smart-seq2 public primer sequence from the Reads (If the length of trimmed Reads is lower than 30bp, reads should be discarded. If it is PE sequence, both of the reads must be removed ); 2) Remove the contaminated reads for adapters (The contaminated reads for adapters was defined that the Read Bases contained more than 5bp of adapter sequences. If either one of the PE Reads was polluted, we will remove both ends of the reads); 3) Remove the low quality reads (The low quality reads was defined that the number of Reads Bases whose phred Quality value was less than or equal to 19 accounted for more than 15% . If either one of the PE Reads defined as low quality, we will remove both ends of the reads); 4) Remove the reads whose N base more than 5% for total bases (If either one of the PE Reads had high Ns bases, we will remove both ends of the reads); Alignment :HISAT2 2.1.0 is the software.--dta –t –p 4 is the parameter.And the mapping reads to genome. Supplementary_files_format_and_content: FPKM
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Submission date |
Oct 21, 2019 |
Last update date |
Oct 22, 2019 |
Contact name |
Yueshan Fan |
E-mail(s) |
fanyueshan@hotmail.com
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Phone |
+86 15122590841
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Organization name |
Tianjin Medical University General Hospital
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Street address |
154 Anshan Road, Tianjin, China
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City |
Tianjin |
ZIP/Postal code |
3000000 |
Country |
China |
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Platform ID |
GPL27644 |
Series (1) |
GSE139133 |
hCMEC/D3 cell line with single atorvastatin,single dexamethasone or low-dexamenthasone and atorvastatin treatment after hematoma injuried |
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Relations |
BioSample |
SAMN13066483 |
SRA |
SRX7026839 |
Supplementary data files not provided |
SRA Run Selector![Help](/coreweb/images/long_help4.gif) |
Raw data are available in SRA |
Processed data are available on Series record |
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