|
| Status |
Public on Feb 22, 2024 |
| Title |
Primary Lung fibroblast, Negative control, biol rep 2 |
| Sample type |
SRA |
| |
|
| Source name |
Primary Lung fibroblast
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Primary Lung fibroblast
treatment: TGFβ1 - / ezetimibe -
|
| Treatment protocol |
At passage 2, the cells were seeded into 60mm cell dishes and incubated overnight. After 1.5 hours of serum starvation with 0.1% fetal bovine serum-supplemented media, 2 ng/ml TGFβ1 and/or 20μM ezetimibe was treated and incubated 24 hours before harvest.
|
| Growth protocol |
Primary human lung fibroblasts were isolated and cultured in EMEM supplemented with 15% fetal bovine serum and antibiotics in humified atmosphere with 5% CO2 at 37℃.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA was harvested using Rneasy mini kit (QIAGEN).
RNA libraries for mRNA (polyA RNA) sequencing were prepared using Illumina stranded mRNA prep kit following the manufacturer's protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 550 |
| |
|
| Description |
processed data file's column name: ./sample2_transcript.bam
|
| Data processing |
Base call files from mRNA sequencing were converted to FASTQ format using BCL Convert v3.10 (Illumina). The adapter sequences were trimmed during this process.
After trimming the raw reads using Trimmomatic v0.39, the paired reads were aligned to the GRCh38 human reference transcriptome (Ensembl release 106) by HISAT2 v.2.2.1.
Alignment counts were summarized using the featureCounts program of the Subread package v.2.0.3.
Data normalization and differential expression analysis were performed using DESeq2 in R.
Assembly: GRCh38 (Ensembl release 106)
Supplementary files format and content: tab-delimited text file includes alignment counts without normalization.
|
| |
|
| Submission date |
Feb 23, 2023 |
| Last update date |
Feb 22, 2024 |
| Contact name |
Chanho Lee |
| E-mail(s) |
[email protected]
|
| Organization name |
Yonsei University College of Medicine
|
| Department |
Department of Internal Medicine
|
| Street address |
50-1 Yonsei-ro
|
| City |
Seodaemun-gu |
| State/province |
Seoul |
| ZIP/Postal code |
03722 |
| Country |
South Korea |
| |
|
| Platform ID |
GPL21697 |
| Series (1) |
| GSE225982 |
Effect of ezetimibe treatment on gene expression of TGFβ1-activated primary human lung fibroblasts |
|
| Relations |
| BioSample |
SAMN33426542 |
| SRA |
SRX19487914 |
