|
Status |
Public on Mar 19, 2015 |
Title |
TCF21 knockdown siRNA technical replicate 2 |
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: TCF21 knockdown 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 |
SRX243754 |
BioSample |
SAMN01923913 |