|
| Status |
Public on Jun 18, 2019 |
| Title |
P91 |
| Sample type |
SRA |
| |
|
| Source name |
PAC1 cell line
|
| Organism |
Rattus norvegicus |
| Characteristics |
cell line: PAC1
cell type: Pulmonary artery smooth muscle cell line
cell differentiation state: Proliferative
treatment: No Doxycycline
|
| Treatment protocol |
For siRNA transfection, differentiated PAC1 cells were seeded at 10e5 cells per well and 24 h later transfected with 90 nM of siRNA (C2/Dharmacon for control and RBPMS siRNA/Stealth siRNA RSS363828/ThermoFisher) and oligofectamine. Cells were transfected 24 h later using lipofectamine 2000 with the same concentration of siRNAs. Total RNA was harvested 48 h after the second hit. For overexpression, three pInducer22-RBPMSA lentiviral populations were generated with dedifferentiated PAC1 cells. Populations were either not treated or treated with Doxycycline at 1μg/ml for 24 h, when total RNA was harvested.
|
| Growth protocol |
Rat PAC1 pulmonary artery SMCs were grown in DMEM supplemented with Glutamax (Invitrogen) and 10% FBS. To encourage the cells toward a more differentiated state they were sub-cultured at a 1:10 dilution once per week and for the more proliferative state they were sub-cultured 1:20 twice per week. (M. Llorian, et al., 2016)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Tri-reagent (Sigma/9424) and Zymo direct-zol columns (Zymo Research/R2050).
Poly A selection using NEB Ultra II kit.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
NEBNext11
PolyA, paired-end 150 mRNA-Seq.
processed data file: Table_TPM_values_per_gene_per_sample.txt
|
| Data processing |
Read Trimming and adapter removal performed with Trimmomatic (version 0.36).
Read alignment and gene expression quantification was performed with RSEM (v 1.2.31) and STAR (v 2.5.2a).
Differential expression analysis was carried out with DESeq2 package (version 1.16.1) with R version 3.4.1.
TPM values were obtained from RSEM (genes.results files).
Alternative splicing analysis was carried out using rMATS version 3.2.5.
Genome_build: Ensembl Rnor_6.0 release-89
Supplementary_files_format_and_content: Table_TPM_values_per_gene_per_sample.txt: Tab-delimited text file includes TPM values for each gene on each sample.
|
| |
|
| Submission date |
Mar 04, 2019 |
| Last update date |
Jun 18, 2019 |
| Contact name |
Christopher WJ Smith |
| E-mail(s) |
cwjs1@cam.ac.uk
|
| Organization name |
University of Cambridge
|
| Department |
Department of Biochemistry
|
| Lab |
Hopkins Building
|
| Street address |
Tennis Court Road
|
| City |
Cambridge |
| ZIP/Postal code |
CB2 1QW |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL22396 |
| Series (2) |
| GSE127799 |
RBPMS knockdown and overexpression in rat PAC1 pulmonary artery smooth muscle cells (SMCs) |
| GSE127800 |
RNA-seq analysis of rat smooth muscle cells |
|
| Relations |
| BioSample |
SAMN11050703 |
| SRA |
SRX5460761 |
