|
| Status |
Public on Apr 25, 2014 |
| Title |
ADF04DF RNA-Seq |
| Sample type |
SRA |
| |
|
| Source name |
normal primary dermal fibroblasts
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: --
cell type: normal primary dermal fibroblasts
|
| Biomaterial provider |
Norwegian Stem Cell Center
|
| Treatment protocol |
Cells were cultured as described under Growth protocol. 2x10e6 cells were cultured to confluency for RNA preparation before harvesting to ensure consistency of cell cycle stages between the two cell types.
|
| Growth protocol |
Human normal dermal fibroblasts (Lonza CC-2511; LDFs) and human normal primary dermal fibroblasts (Norwegian Stem Cell Center AD04DFs) were cultured in DMEM/F12 containing 13% FCS, 2 ng/ml basic fibroblast growth factor and antibiotics. Cells were exponentially growing and used at passage 5-7. AD04DFs were obtained with Norwegian Ethics Committee Approval REK2617A.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using the Ambion TRIzol® Reagent RNA extraction kit (Life Technologies), quality checked using a BioAnalyzer 2100 and processed for library preparation.
RNAseq library was prepared according to the Illumina protocol, and sequenced on an Illumina HiSeq2500 at the Norwegian Sequencing Center.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
reads aligned with tophat v2.0.8b with parameter –no-novel-juncs
transcript abundance estimated with cufflinks v2.1.1 with parameter –GTF
csv file created from column 5 and 10 from cufflinks output file genes.fpkm_tracking
Genome_build: hg19
Supplementary_files_format_and_content: csv with two columns; gene_short_name and fpkm value
|
| |
|
| Submission date |
Jan 23, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Philippe Collas |
| Organization name |
University of Oslo
|
| Department |
Institute of Basic Medical Sciences
|
| Street address |
PO Box 1112 Blindern
|
| City |
Oslo |
| ZIP/Postal code |
0317 |
| Country |
Norway |
| |
|
| Platform ID |
GPL16791 |
| Series (2) |
| GSE54333 |
EDD: a program for detection of wide genomic enrichment domains robust against local variations [RNA-Seq] |
| GSE54334 |
EDD: a program for detection of wide genomic enrichment domains robust against local variations |
|
| Relations |
| BioSample |
SAMN02595207 |
| SRA |
SRX447391 |
