|
| Status |
Public on Jan 13, 2017 |
| Title |
Normal Fibroblasts vehicle treated |
| Sample type |
SRA |
| |
|
| Source name |
NF4FBS
|
| Organism |
Homo sapiens |
| Characteristics |
1,25d treatment: Vehicle (FBS) treatment for 24 h
cell type: normal human primary fibroblasts
|
| Treatment protocol |
Vitamin D (1,25D 100 nM) resuspended in FBS was added to NF growing in culture. FBS alone was added to the control sample. 24 h after initiating treatment, cells were collected, and RNA extracted.
|
| Growth protocol |
Normal human primary fibroblasts (NF) were grown in culture in complete DMEM-HG media, containing 10% FBS, antibiotic, and antimycotics.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
NF supplemented with 10-7 M 1,25D (1α,25-dihydroxyvitamin D3; Sigma-Aldrich) or FBS for 24 h using Aurum Total RNA Mini Kit (Bio-Rad) with DNaseI treatment following the manufacturer’s protocol.
Ion Xpress IonXpressRNA barcoded sequencing libraries were constructed using the Eukaryotic Ribominus and Ion Total v2 kits (Life Technologies) according to the manufacturer's directions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Ion Torrent Proton |
| |
|
| Data processing |
Basecalling and quality filtering was performed by Torrent Suite version 4 software using the default settings
Alignment to human genome sequence was performed using TMAP map4 algorithm with 5' and 3' softclipping and a minimum seed length of 20 nt
The strand specific total sequencing base pair coverage in all exons was summed for all annotated genes in each sample and normalized to total coverage using bedtools, custom R code, and Microsoft Excel as described in Wu et al. 2015 PLoS Genetics Nov 6;11(11):e1005655.
Strand-specific bedgraph files of genome coverage for each sample were generated using BEDTools.
Genome_build: Homo sapiens release hg19
Supplementary_files_format_and_content: File with normalized basepair coverage for annotated genes with > 1000 base pair total coverage in all samples, and non-normalized strand-specific bedgraph files of genome coverage for each individual sample.
|
| |
|
| Submission date |
Jan 14, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Susana Gonzalo |
| E-mail(s) |
[email protected]
|
| Phone |
314-997-9244
|
| Organization name |
Saint Louis University
|
| Department |
Biochemistry and Molecular Biology
|
| Street address |
1100 S Grand Blvd
|
| City |
St Louis |
| State/province |
MO |
| ZIP/Postal code |
63104 |
| Country |
USA |
| |
|
| Platform ID |
GPL17303 |
| Series (2) |
| GSE76883 |
Vitamin D/Vitamin D Receptor (VDR) Axis Regulates LMNA gene expression [RNA-Seq] |
| GSE76887 |
Vitamin D/Vitamin D Receptor (VDR) Axis Regulates LMNA gene expression |
|
| Relations |
| BioSample |
SAMN04414860 |
| SRA |
SRX1531618 |
