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| Status |
Public on Jan 21, 2021 |
| Title |
69-7_P8 Blood |
| Sample type |
SRA |
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| Source name |
Blood
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| Organism |
Homo sapiens |
| Characteristics |
cell type code: P8
cell type: B7+ CD8
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| Extracted molecule |
total RNA |
| Extraction protocol |
2000 sorted cells were flash frozen in 300 ul of RLT buffer and extracted using the Qiagen mini lipid RNA isolation kit according to manufacturers 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.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
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| 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.
Supplementary_files_format_and_content: Tables of normalized counts per gene. Comparison between tissue types and characteristics.
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| Submission date |
Jan 20, 2021 |
| Last update date |
Jan 22, 2021 |
| Contact name |
Smita Iyer |
| E-mail(s) |
smiyer@ucdavis.edu
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| Organization name |
University of California-Davis
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| Department |
Center for Immunology and Infectious Disease
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| Street address |
county rd 98 & hutchison, ccm room 2075
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| City |
Davis |
| State/province |
CA |
| ZIP/Postal code |
95616 |
| Country |
USA |
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| Platform ID |
GPL20301 |
| Series (1) |
| GSE165213 |
RNA seq of sorted T cell subsets from PBMCs and rectal biopsies from humans and rhesus macaques |
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| Relations |
| BioSample |
SAMN17391442 |
| SRA |
SRX9904623 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5028393_69-7_P8_host-rs_alaHtseq.txt.gz |
270.5 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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