|
| Status |
Public on Feb 24, 2016 |
| Title |
hsa_ControlKBC3_RNASeq |
| Sample type |
SRA |
| |
|
| Source name |
human superficial temporal artery tissue
|
| Organism |
Homo sapiens |
| Characteristics |
subject status: patients undergoing craniotomy for cerebral aneurysms
subject/sample id: KBC3
tissue: human superficial temporal artery tissue
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA-Seq collected from human cerebral aneurysm tissue. RNA was harvested from patient samples using mirVana miRNA isolation kit, allowing total RNA to be isolated containing the miRNA population
RNA was fragmented prior to adaptor ligation, reverse transcription was performed, and the resulting cDNA was purified and amplified.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Ion Torrent Proton |
| |
|
| Description |
RNA-Seq collected from human cerebral aneurysm tissue. RNA was harvested from patient samples using mirVana miRNA isolation kit, allowing total RNA to be isolated containing the miRNA population.
|
| Data processing |
Reads were sequenced on the IonTorrent Proton
RNA quality and quantity were assessed by Fragment Analyzer (Advanced Analytical, Ames, IA) and Qubit (Invitrogen, Carlsbad, CA), respectively.
Reads were trimmed as part of the IonTorrent pipeline.
RNA-Seq fastq files were aligned to the iGenomes bowtie2 index for hg19 using TopHat v2.0.9, using the iGenomes gtf file for human ENSEMBL genes, and --no-novel-juncs and --no-coverage-search
Differential expression was measured with cuffdiff v2.2.1 with default parameters, and using the reference transcriptome GTF file from iGenome for hg19.
Genome_build: hg19
Supplementary_files_format_and_content: Computed with Cuffdiff v2.2.1 with default parameters, and using the reference transcriptome GTF file from iGenome.
|
| |
|
| Submission date |
Feb 26, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
David Anthony Hendrix |
| E-mail(s) |
david.hendrix@oregonstate.edu
|
| Phone |
(541) 737-6224
|
| Organization name |
Oregon State University
|
| Department |
Biochemistry and Biophysics/EECS
|
| Street address |
2011 Ag & Life Sciences Bldg
|
| City |
Corvallis |
| State/province |
OR |
| ZIP/Postal code |
97331 |
| Country |
USA |
| |
|
| Platform ID |
GPL17303 |
| Series (2) |
| GSE66238 |
MicroRNA and gene expression changes in human cerebral aneurysms [RNA-seq] |
| GSE66240 |
MicroRNA and gene expression changes in human cerebral aneurysms |
|
| Relations |
| BioSample |
SAMN03376172 |
| SRA |
SRX891624 |
