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Sample GSM4131420

Query DataSets for GSM4131420

Status

Public on Oct 22, 2019

Title

11D2-1

Sample type

SRA

Source name

hCMEC/D3 cell lines

Organism

Homo sapiens

Characteristics

tissue: brain vascular
cell type: temporal lobe microvessels
agent: single dexamethasone

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.

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.

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

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina NovaSeq 6000

Description

11D2-1

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

Submission date

Oct 21, 2019

Last update date

Oct 22, 2019

Contact name

Yueshan Fan

E-mail(s)

fanyueshan@hotmail.com

Phone

+86 15122590841

Organization name

Tianjin Medical University General Hospital