|
| Status |
Public on Nov 06, 2014 |
| Title |
150_day_Quiescence_3 |
| Sample type |
SRA |
| |
|
| Source name |
total RNA extracted from MRC-5 fibroblasts
|
| Organism |
Homo sapiens |
| Characteristics |
population doublings: 36
cell type: MRC-5 fibroblasts
treatment: subjected to quiescence using 150 days contact inhibition
|
| Treatment protocol |
MRC-5 fibroblastswere subjected to quiescence using 150 days contact inhibition
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using QIAzol (Qiagen, Hilden, Germany) based on the phenol/chloroform extraction method. Afterwards the RNA was quantified photometrically with a NanoDrop 1000 (PeqLab, Erlangen, Germany) and stored at -80 °C until use.
For library preparation an amount of 2 μg of total RNA per sample was processed using Illumina’s TruSeqTM RNA Sample Prep Kit (Illumina; San Diego; CA, USA) following the manufacturer’s instruction.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Illumina Casava software used for extraction of FASTQ files
FASTQ files were mapped using Tophat (v2.0.6) vs. the H.sapiens genome GRCh37.66 obtained from Ensembl
Uniquely mapped reads were counted for each gene_id using featureCounts (featureCounts -T 8 -a $GTF -s 0 -t exon -g gene_id -o featureCounts_gene.txt $SAMFILE)
RPKM values were computed using exon lengths provided by featureCounts and the sum of all mapped reads per sample
Genome_build: GRCh37.p6
Supplementary_files_format_and_content: Excel file including raw counts and RPKM values for each sample
|
| |
|
| Submission date |
Aug 28, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
JenAge Project |
| E-mail(s) |
geo-data@jenage.de
|
| Organization name |
Leibniz Institute for Age Research - Fritz Lipmann Institute
|
| Street address |
Beutenbergstr. 11
|
| City |
Jena |
| ZIP/Postal code |
D-07745 |
| Country |
Germany |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE60883 |
RNA-seq of young and quiescent MRC-5 human fibroblasts |
|
| Relations |
| BioSample |
SAMN03012549 |
| SRA |
SRX689255 |
