|
| Status |
Public on Sep 22, 2016 |
| Title |
Tricuspid aortic valve_calcified_YBO054 |
| Sample type |
SRA |
| |
|
| Source name |
Human aortic valve leaflet
|
| Organism |
Homo sapiens |
| Characteristics |
age: 58
gender: Male
tissue: Calcified tricuspid aortic valve (TAV)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from 30 mg and 100 mg of normal and calcified tissue, respectively, using a modified TRIzol protocol followed by RNA cleanup using QIAGEN RNeasy Mini Kit. Illumina TruSeq RNA Sample Prep Kit was used with 2 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
duplicate of GSM1338130
|
| Data processing |
Illumina CASAVA software used for basecalling.
Sequenced reads were trimmed for adaptor sequence and then mapped to Hg19 whole genome using tophat v2.0.9-1 (-r85 --mate-std-dev 75) and bowtie v1.0.0-1 (Trapnell, Nat Biotechnol. 2013;31:46-53)
The aligned reads were assembled by Cufflinks program to produce transcripts annotated to the same reference genome. The tool Cuffdiff of Cufflinks was utilized to quantify the transcriptomes and compare them across calcified and normal tricuspid valves (Trapnell, Nat Biotechnol. 2013;31:46-53).
Genome_build: Hg19
Supplementary_files_format_and_content: Tab-delimited text files include genes FPKMs and isoforms FPKMs.
|
| |
|
| Submission date |
Jan 11, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Sandra Guauque-Olarte |
| E-mail(s) |
sandra-milena.guauque.1@ulaval.ca
|
| Phone |
418-6568711
|
| Organization name |
CRIUCPQ
|
| Street address |
2725, chemin Sainte-Foy
|
| City |
Quebec |
| ZIP/Postal code |
G1V 4G5 |
| Country |
Canada |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE76717 |
RNA Expression Profile of Calcified Bicuspid, Tricuspid and Normal Human Aortic Valves by RNA Sequencing [TAV] |
| GSE76718 |
RNA Expression Profile of Calcified Bicuspid, Tricuspid and Normal Human Aortic Valves by RNA Sequencing |
|
| Relations |
| Affiliated with |
GSM1338130 |
| BioSample |
SAMN04395652 |
| SRA |
SRX1526942 |
