|
| Status |
Public on Sep 20, 2018 |
| Title |
R24Sil_RCt14_RM_SIV_SC_D28_1_Mono_RLT_mRNA_Seq_S4 |
| Sample type |
SRA |
| |
|
| Source name |
Sorted Monocytes Infected with SIV
|
| Organism |
Macaca mulatta |
| Characteristics |
infected: Infected with SIV
animal id: RCt14
timepoint: Day 28
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 28
|
| 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) |
[email protected]
|
| 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 |
SAMN08622757 |
| SRA |
SRX3750972 |
