|
| Status |
Public on Sep 09, 2020 |
| Title |
Hippocampus [SI03H] |
| Sample type |
SRA |
| |
|
| Source name |
Brain Tissue
|
| Organism |
Macaca mulatta |
| Characteristics |
tissue: Hippocampus
gender: Female
treatment: Control- Perfused
|
| Treatment protocol |
N/A
|
| Growth protocol |
N/A
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Different parts of brain tissues were collected from perfused animals. Collected cells were flash frozen in RLT buffer and extracted using the Qiagen mini lipid RNA isolation kit according to manufacturer's instructions.
The libraries were constructed following the 3' TagSeq protocol using Lexogen kit (QuantSeq 3’ mRNA-Seq Library Prep Kit FWD for Illumina). 500ng of total RNA was used as input.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
SI03H
44003
3′-Tag-Seq
counts_all.out
|
| Data processing |
The raw read data was filtered using HTStream (version 1.3.1) which included screening for contaminants (such as PhiX and rRNA), quality-based trimming, and adapter trimming. (https://github.com/s4hts/HTStream)
STAR (version 2.7.3a) was used to align the processed data to the rhesus genome (Mmul_10). Dobin, Alexander, et al. "STAR: ultrafast universal RNA-seq aligner." Bioinformatics 29.1 (2013): 15-21.
MultiQC (custom version) was then used for read and alignment quality assessment. https://github.com/s4hts/MultiQC
Differential expression analyses were conducted using the limma-voom Bioconductor pipeline, using edgeR version 3.30.3 and limma version 3.44.3 in R 4.0.1 The model used in limma included effects for brain region, infection status, and their interaction, and standard errors of log fold changes were adjusted for within-animal correlations.
Genome_build: Mmul_10
Supplementary_files_format_and_content: counts_all.out.txt: Table of normalized counts per gene.
Supplementary_files_format_and_content: Comparison between tissue types and characteristics.
|
| |
|
| Submission date |
Sep 08, 2020 |
| Last update date |
Sep 09, 2020 |
| Contact name |
Smita Iyer |
| E-mail(s) |
smiyer@ucdavis.edu
|
| Organization name |
University of California-Davis
|
| Department |
Center for Immunology and Infectious Disease
|
| Street address |
county rd 98 & hutchison, ccm room 2075
|
| City |
Davis |
| State/province |
CA |
| ZIP/Postal code |
95616 |
| Country |
USA |
| |
|
| Platform ID |
GPL23949 |
| Series (1) |
| GSE157690 |
RNA-seq of select neural tissue in SHIV infected and control rhesus macaques |
|
| Relations |
| BioSample |
SAMN16083843 |
| SRA |
SRX9096554 |
