|
| Status |
Public on Nov 16, 2018 |
| Title |
53_68YR_Male_Caucasian |
| Sample type |
SRA |
| |
|
| Source name |
Skin; Arm
|
| Organism |
Homo sapiens |
| Characteristics |
cell id: AG12850
disease: Normal
Sex: Male
age: 68
ethnicity: Caucasian
|
| Growth protocol |
Human dermal fibroblasts documented as ‘apparently healthy individuals’ deposited from the National Institute of Aging or the NIGMS Human Genetic Cell Repository were obtained or purchased from the Coriell Biobank Cell Repository (Camden, New Jersey, USA). The cells were cultured in high-glucose (4.5mg/ml) DMEM (Gibco) supplemented with 15% (vol/vol) fetal bovine serum (Gibco), 1X glutamax (Gibco), 1X non-essential amino acids (Gibco) and 1% (vol/vol) penicillin-streptomycin (Gibco). HGPS patient fibroblasts were obtained from the Progeria Research Foundation and were cultured in high-glucose (4.5mg/ml) DMEM (Gibco) supplemented with 20% (vol/vol) fetal bovine medium and 1% (vol/vol) penicillin-strepomycin. All fibroblasts were cultured in DMEM unless specified and were maintained at 37oC in a humidified incubator with 3% O2 and 7.5% CO2. Cells were passaged every 2 to 5 days at 85% confluence.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using 1ml of TriZol reagent (Invitrogen) directly from the six-well plates or trypsinized and pelleted from 100mm dishes. RNA was purified with RNeasy Mini kits with 30 minutes of DNase I treatment to remove Genomic DNA in accordance to the manufacturer’s instructions (Qiagen).
mRNA sequence libraries were prepared using the Illumina TruSeq Stranded mRNA kit with 150ng-1ug of total RNA.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
fpkm.txt
|
| Data processing |
Reads were aligned to the human genome (hg19) using STAR (version 2.5.1b)
Only reads that aligned uniquely to a single genomic location were used for downstream analysis (MAPQ > 10 ).
Gene expression (FPKM) values were calculated for annotated RefSeq genes using HOMER (V4.9.1) by counting reads found overlapping exons
The top expressed isoform was used as proxy for gene expression, resulting in 27,142 unique genes.
Age prediction models were fit to the FPKM data for all subjects using leave-one-out cross-validation. Model performance is reported on the average error made on the held-out sample for each validation fold.
Genome_build: hg19
Supplementary_files_format_and_content: FPKM expression table
|
| |
|
| Submission date |
May 02, 2018 |
| Last update date |
Mar 28, 2022 |
| Contact name |
April Elizabeth Williams |
| E-mail(s) |
apriljack06@gmail.com, awilliams@salk.edu
|
| Phone |
7345461645
|
| Organization name |
Salk Institute for Biological Studies
|
| Department |
IGC
|
| Street address |
10010 N Torrey Pines Rd
|
| City |
San Diego |
| State/province |
California |
| ZIP/Postal code |
92037 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE113957 |
Predicting age from the transcriptome of human dermal fibroblasts |
|
| Relations |
| BioSample |
SAMN09011881 |
| SRA |
SRX4022495 |
