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Sample GSM3148561 Query DataSets for GSM3148561
Status Public on Mar 20, 2019
Title Sample_Baboon_8024_lowLDL_chow-RNA_seq_1
Sample type SRA
 
Source name WBC
Organism Papio hamadryas
Characteristics tissue: Blood
barcode: CGATGT
Treatment protocol Total RNA siolated using Trizol and Quigen reagents.
Growth protocol Baboon blood collected, buffy coat isolated and stored in -80 freezer.
Extracted molecule total RNA
Extraction protocol Libraries were constructed with the Illumina Paired-End Cluster Generation Kitv4 (2x100bp)
RNA Seq; two files per run included
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Description Libraries were constructed with the Illumina Paired-End Cluster Generation Kitv4 (2x100bp)
Data processing Basecalls performed using CASAVA version 1.8
The sequencing output FASTQ files were analyzed using default settings of Partek Flow (Partek Inc., MO).
The sequence reads were aligned with STAR aligner v2.3.1j to baboon transcriptome (Ensembl PapAnu2 release 76).
To quantify the expression levels of transcripts, the mapped reads were normalized (reads assigned per kilobase of target per million mapped reads, RPKM) and quantified using Partek’s expectation maximization (EM) algorithm. Differential expression of genes was evaluated using Partek’s gene specific analysis (GSA).
Genome_build: Ensembl PapAnu2 release 76
Supplementary_files_format_and_content: fastq
 
Submission date May 21, 2018
Last update date Mar 20, 2019
Contact name Genesio Karere
E-mail(s) gkarere@wakehealth.edu
Organization name Wake Forest Baptist Health Sciences
Department Internal Medicne
Street address 1 medical center blvd
City Winston-Salem
State/province NC
ZIP/Postal code 78227
Country USA
 
Platform ID GPL25014
Series (1)
GSE114722 Identification of coordinately regulated microRNA-gene networks that differ in baboons discordant for LDL-Cholesterol
Relations
BioSample SAMN09232577
SRA SRX4108292

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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