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Sample GSM1619678 Query DataSets for GSM1619678
Status Public on Feb 24, 2016
Title hsa_ControlKBC14_R1_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: KBC14
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 SAMN03376179
SRA SRX891620

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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