|
| Status |
Public on Oct 23, 2014 |
| Title |
13L RNA-seq |
| Sample type |
SRA |
| |
|
| Source name |
primary skin fibroblast, late timepoint (L)
|
| Organism |
Homo sapiens |
| Characteristics |
age (yr): 75
tissue: primary skin fibroblast
time point: late timepoint (L)
|
| Growth protocol |
Primary Skin Fibroblast cells were grown with culture medium (DMEM supplemented with 6% fetal bovine serum) for 2 -3 passages.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from human skin fibroblasts was prepared using PureLink RNA Mini kit (Ambion, Cat#12183018A). The cells were lysed by addition of lysis buffer, the lysate was then homogenized using QIAshredder (QIAGEN, cat# 79654) by centrifugation at 14,000g for 2 min, and then processed following the manufacturer's instructions. The isolated total RNA was aliquoted, and the quality of the prepared RNA was evaluated using Bioanalyzer. The RNA samples were used for RNA-seq with a range of RIN values between 8.50 and 10. A cDNA library for deep sequencing was prepared using oligo d(T) primer. The Illumina protocol (kit) was followed for later steps.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Illumina Casava1.8 software used for basecalling.
Transcripts assembly was done for individual sample by using tophat v2.0.6 (default parameters; PMID 23618408) and cufflinks v2.1.1 (default paramters; PMID: 23222703) against hg19 genome sequence and using GENCODE version 16 as GTF guidance reference file. Transcripts from all non-strand-specific-RNA-Seq samples were then merged by using cuffmerge v1.0.0 (default paramters).
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample as defined by cufflinks
|
| |
|
| Submission date |
Oct 21, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Marc Jung |
| E-mail(s) |
[email protected]
|
| Organization name |
City Of Hope
|
| Department |
Biology
|
| Lab |
Gerd Pfeifer
|
| Street address |
1500 East Duarte Street
|
| City |
Duarte |
| State/province |
CA |
| ZIP/Postal code |
91010 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE51518 |
RNA-seq from primary skin fibroblasts, derived of matched pairs of middle and late donor age |
| GSE51519 |
Aging signatures developed from a longitudinal study design are dominated by reduced transcription of genes involved in protein synthesis. |
|
| Relations |
| BioSample |
SAMN02378886 |
| SRA |
SRX366403 |
