|
Status |
Public on Mar 20, 2019 |
Title |
Sample_Baboon_6910_lowLDL_chow_RNA_seq_7 |
Sample type |
SRA |
|
|
Source name |
WBC
|
Organism |
Papio hamadryas |
Characteristics |
tissue: Blood barcode: AGTCAA
|
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 |
SAMN09232580 |
SRA |
SRX4108290 |