|
| Status |
Public on May 18, 2016 |
| Title |
D4-1IL: IL1α 4 |
| Sample type |
SRA |
| |
|
| Source name |
venous smooth muscle cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: primary venous smooth muscle cells
passage: p4-5
treatment: 0.2% serum + 10ng/ml IL1α
|
| Treatment protocol |
Cells were quiesced in 0.2% serum for 48h followed by addition of 10ng/ml IL1α , 20ng/ml PDGF or both 10ng/ml IL1α and 20ng/ml PDGF together for 72h.
|
| Growth protocol |
venous smooth muscle cells were used between passage 4 and 5. Cells (1x105/well) were cultured and plated in uncoated 6 well plates in 15%FBS Smooth Muscle Cell Growth Medium 2 (PromoCell, Heidelberg, Germany) and left to adhere for 24h.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were lysed with qiazol and RNA fractation removed following addition of chloroform, further extraction was completed using Qiagen miRNeasy kit according to manufacturers protocol
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
molecule: rRNA depleted RNA
IL1α treatment is group2 in edgeR analysis
|
| Data processing |
Adapter sequences trimmed with Flexbar version 2.4
mapping was performed with Tophat version 2.0.9 in conjunction with Bowtie version 1.0.0.
Cufflinks version 2.1.1 was used to detect known and predicted genes and transcripts from the Ensembl gene models for the grch37 release of the human genome. Cuffdiff version 2.1.1 was used to collect FPKM expression values for samples which were run as experimental groups.
For differential expression, the edgeR R Bioconductor 2.12 package was used with the use of the easyRNASeq R Bioconductor package to establish raw read counts from the Tophat2 generated BAM alignment files
Genome_build: GRCh37
Supplementary_files_format_and_content: cpm.csv file contains raw cpm for each gene in each sample. edgeR.csv files contain comparison between groups: logFC, logCPM, p value and FDR
|
| |
|
| Submission date |
Jun 07, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Rachel Dakin |
| E-mail(s) |
rachel.dakin@glasgow.ac.uk
|
| Phone |
01413303301
|
| Organization name |
University of Glasgow
|
| Department |
ICAMS
|
| Street address |
126 University Place
|
| City |
Glasgow |
| ZIP/Postal code |
G12 8TA |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE69637 |
RNA-seq identifies novel lncRNAs involved in vascular smooth muscle cell proliferation |
|
| Relations |
| BioSample |
SAMN03764427 |
| SRA |
SRX1052073 |
