|
| Status |
Public on Aug 10, 2016 |
| Title |
sample8: FBs cultured in Apoa1 |
| Sample type |
SRA |
| |
|
| Source name |
dermal fibroblasts
|
| Organism |
Mus musculus |
| Characteristics |
background strain: C57BL/6
cell type: dermal fibroblast of adult skin
passages: P3-5
|
| Treatment protocol |
Fibroblasts were cultured with the indicated proteins (the concentration of each protein was 0.01 μg/ml) or E16.5 skin extract (2 μg/ml) for 3 days.
|
| Growth protocol |
All fibroblasts and DP cells were expanded and cultured in DMEM with 10% FBS
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Totoal RNA was extracted using Qiagen RNeasy kit(Cat No./ID: 74104) according to the manufacturer's protocol
Total 1~2 g RNA was purified by using poly-T oligo-attached magnetic beads.The cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers. Paired-end 150 nucleotide reads from each mRNA library were obtained using NextSeq500 (Illumina Inc., CIC bioGUNE, Bilbao, Spain).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
RNA-seq reads were aligned to mm10 genome assembly using Tophat version 2.0.9 with parameters -p 12 --library-type fr-firststrand
Cufflinks verson 2.2.1 was then applied to assemble transcripts and quantify their abundance in terms of FPKM (fragments per kilobase of transcript per million fragments mapped)
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
|
| |
|
| Submission date |
Aug 08, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Mai-Yi Fan |
| E-mail(s) |
s.maiyifan@gmail.com
|
| Organization name |
National Taiwan University
|
| Street address |
No1, Sec. 1, Jen - Ai Rd.
|
| City |
Taipei |
| ZIP/Postal code |
100 |
| Country |
Taiwan |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE85303 |
RNAseq changes in fibroblasts after treatment with selected protein(s) or E16.5 skin extract |
|
| Relations |
| BioSample |
SAMN05513559 |
| SRA |
SRX2006711 |
