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Sample GSM3314485 Query DataSets for GSM3314485
Status Public on Jul 21, 2021
Title Normal fibroblasts vc at day 5 16-13585
Sample type SRA
 
Source name Dermal fibroblasts
Organism Homo sapiens
Characteristics cell type: primary normal dermal fibroblasts
passages: 5-10
treatment: vehicle control (vc)
time: Day 5 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 Normal fibroblasts vc at day 5 16-13585 16-13585
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 SAMN09741953
SRA SRX4488027

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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