|
| Status |
Public on Mar 19, 2015 |
| Title |
non-silencing control siRNA technical replicate 1 |
| Sample type |
SRA |
| |
|
| Source name |
in vitro cultured primary coronary artery smooth muscle cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: in vitro cultured primary coronary artery smooth muscle cells
transfection: non-silencing control siRNA
|
| Treatment protocol |
HCA-SMCs were transfected with 300 nM TCF21 Trilencer-27 Human siRNA (OriGene #SR304753C) or Trilencer-27 Universal Scrambled Negative Control siRNA (OriGene #SR30004) at 80% confluence using the Amaxa Basic Nucleofector Kit for Primary Mammalian Smooth Muscle Cells (Lonza #VPI-1004). Cells were transfected following the Lonza Optimized Protocol for Primary Mammalian Smooth Muscle cells at a density of 1 x 106 cells per 100 µL sample using Nucleofector Program U-025. Cells were changed to medium without supplements at 18 hours post-transfection and cultured for an additional 48 hours.
|
| Growth protocol |
SmGM-2 Smooth Muscle Growth Medium-2 including hEGF, insulin, hFGF-B and FBS, but without antibiotics
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from cultured HCASMCs was obtained by direct lysis using the QIAGEN miRNeasy Mini Kit (Qiagen #217004) according to manufacturer’s instructions.
Total RNA of 3 samples each either siTCF21 or siControl treated samples was depleted for ribosomal RNA with the Ribo-Zero magnetic kit from epicentre (Illumina #MRZH116), libraries generated with the epicentre ScriptSeq v2 RNA-Seq library preparation kit (Illumina #SSV21106).
Libraries were sequenced as 100bp paired-end reads on an Illumina HiSeq 2000 instrument.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
alignment: tophat
alignment: bowtie
transcript assembly: cufflinks
differential assembly: cuffdiff
genome build: Hg19 male
processed data files format and content: bed
|
| |
|
| Submission date |
Feb 21, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Sylvia T Nurnberg |
| E-mail(s) |
sylvian@upenn.edu
|
| Organization name |
University of Pennsylvania
|
| Department |
Medicine
|
| Lab |
Rader
|
| Street address |
3400 Civic Center Blvd
|
| City |
Philadelphia |
| State/province |
PA |
| ZIP/Postal code |
19104 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE44461 |
Coronary Artery Disease Associated Transcription Factor TCF21 Regulates Smooth Muscle Precursor Cells that Contribute to the Fibrous Cap |
|
| Relations |
| SRA |
SRX243750 |
| BioSample |
SAMN01923909 |
