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Sample GSM3026851 Query DataSets for GSM3026851
Status Public on Sep 20, 2018
Title R24Sil_RMe14_RM_SIV_SC_D14_1_Mono_RLT_mRNA_Seq_S11
Sample type SRA
 
Source name Sorted Monocytes Infected with SIV
Organism Macaca mulatta
Characteristics infected: Infected with SIV
animal id: RMe14
timepoint: Day 14
library batch: 1
cell type: Monocytes
Treatment protocol please refer to https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4097788/
Growth protocol please refer to https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4097788/
Extracted molecule total RNA
Extraction protocol mRNA was isolated using the QIAGEN miRNeasy Kit.
Whole transcriptome libraries were constructed using the TruSeq Stranded Total RNA with Ribo-Zero Gold (Illumina, San Diego, CA) according to the manufacturer’s guide. Libraries were quality controlled and quantitated using the BioAnalzyer 2100 system and qPCR (Kapa Biosystems, Woburn, MA).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Description Sorted Monocytes Infected with SIV at Day 14
Data processing Constructed libraries were sequenced on an NextSeq 500 Illumina platform, producing 2x75nt stranded paired end reads (52 Gb). Image analysis, base calling, and error estimation were performed using Illumina Analysis Pipeline (version 2.8).
Quality control of the primary sequencing data was performed using FastQC (version 0.11.3) and included adapter trimming using cutadapt (version 1.8.3).
Reads were aligned using STAR (version 2.4.2)
Ensembl build Mmul_1 using illumina's igenomes resource
We mapped reads to the genome Macaca mulatta genome (build Mmul_1) with STAR. After mapping, we assigned aligned read counts from BAM files to exons and genes using the python package HT-Seq (version 0.6.1).  HT-Seq provided the most accurate way of aligning read counts to overlapping exons. Reads that mapped to multiple positions were removed.
Genome_build: Macaca mulatta Ensembl (build Mmul_1) from illumina's igenomes resource: https://support.illumina.com/sequencing/sequencing_software/igenome.html
Genome_build: Chlorocebus_sabeus 1.0 from https://www.ncbi.nlm.nih.gov/assembly/GCA_000409795.1/
Supplementary_files_format_and_content: Two raw count matrix of files generated with ht-seq is attached
 
Submission date Feb 28, 2018
Last update date Sep 20, 2018
Contact name Michael Gale, Jr
E-mail(s) uw_galelab_geo@uw.edu
Organization name University of Washington
Department Immunology
Street address 750 Republican St. E360, Box 358059
City Seattle
State/province Washington
ZIP/Postal code 98109
Country USA
 
Platform ID GPL21120
Series (2)
GSE111233 Wound healing mechanisms in pathogenesis control in natural SIV host species [monocytes]
GSE111234 Wound healing mechanisms in pathogenesis control in natural SIV host species
Relations
BioSample SAMN08622750
SRA SRX3750978

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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