|
| Status |
Public on Jul 21, 2021 |
| Title |
Keloid fibroblasts vc at day 1 KeloidVC2 |
| Sample type |
SRA |
| |
|
| Source name |
Dermal fibroblasts
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: primary keloid dermal fibroblasts
passages: 5-10
treatment: vehicle control (vc)
time: Day 1 after treatment
tissue: Human skin
|
| Treatment protocol |
After serum starving, normal and keloid fibroblasts were cultured for 1 or 5 days with/without follistatin treatment.
|
| Growth protocol |
Biopsy samples were finely minced and plated out for culture in T25 or T75 flasks. Primary human dermal fibroblasts were grown in DMEM/F12 (Gibco, Cat# 11039021, Scoresby, Australia) containing 10% Fetal Bovine Serum (Gibco, Cat# 10437028, Scoresby, Australia) and 1% Penicillin-Streptomycin (5,000 U/mL) (Gibco, Cat# 15070063, Scoresby, Australia). All fibroblasts were cultured at 37°C in 5% CO2 and media were changed twice a week.
When cultures reached between 80 and 90% confluency, fibroblasts were plated in 10 cm dishes (Corning, Melbourne, Australia) at a concentration of 3 x 10^5 cells / 10 ml per dish and starved for 24 hours prior to treatment.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA were extracted using RNeasy Mini Kit according to manufacturer's instructions.
Libraries were prepared according to Illumina's instructions at MHTP Medical Genomics Facility.
RNA-seq at MHTP Medical Genomics Facility
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Description |
Keloid fibroblasts vc at day 1 KeloidVC2 KeloidVC2
|
| Data processing |
Data was processed with RNAsik pipeline (https://github.com/MonashBioinformaticsPlatform/RNAsik-pipe - unknown version).
Each fastq file was mapped to reference genome using STAR
Aligned BAM files were then counted against GTF using featureCounts
The raw counts file was loaded into Degust (http://degust.erc.monash.edu/) for differential gene expression analysis
Genome_build: Ensembl reference genome is Homo_sapiens.GRCh38.dna_sm.primary_assembly.fa, GTF file was Homo_sapiens.GRCh38.85.gtf.gz
Supplementary_files_format_and_content: tab seperated file containing the raw counts for each sample
|
| |
|
| Submission date |
Jul 30, 2018 |
| Last update date |
Jul 21, 2021 |
| Contact name |
Seungmin Ham |
| E-mail(s) |
jimmy.ham@monash.edu
|
| Organization name |
Monash University
|
| Department |
Obstetrics and Gynaecology
|
| Street address |
27-31, Wright Street
|
| City |
Clayton |
| State/province |
Victoria |
| ZIP/Postal code |
3168 |
| Country |
Australia |
| |
|
| Platform ID |
GPL21290 |
| Series (1) |
| GSE117887 |
A new understanding of the molecular pathway in human keloid fibroblasts and development of a novel treatment |
|
| Relations |
| BioSample |
SAMN09741962 |
| SRA |
SRX4488018 |
