|
| Status |
Public on Apr 09, 2020 |
| Title |
HIV4 GC |
| Sample type |
SRA |
| |
|
| Source name |
Lymph node
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Germinal Center B Cell
infection: HIV-infected
donor: HIV4
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were FACS sorted directly into Trizol LS and RNA was isolated using the Zymo Clean and Concentrator kit
Libraries were constructed using the NuGen Ovation SoLo RNA-seq system per the manufacturer's instructions
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 550 |
| |
|
| Description |
HIV4:GC_HIV
|
| Data processing |
bcl files were converted to FASTQ using bcl2fastq v 2.17.1.14
Reads were mapped and counted using STAR v2.5.2
Variance stabilized gene counts and differential gene expression was determined by DEseq2
Genome_build: UCSC hg19
Supplementary_files_format_and_content: tab-delimited text file contains raw read counts for all samples
|
| |
|
| Submission date |
Aug 30, 2018 |
| Last update date |
Apr 10, 2020 |
| Contact name |
James Wesley Austin |
| Organization name |
NIH
|
| Street address |
9000 Rockville Pike, Bldg 10, Room 6A05
|
| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
| |
|
| Platform ID |
GPL21697 |
| Series (1) |
| GSE119234 |
Analysis of gene expression differences in lymph node B cell populations of HIV-infected and uninfected controls |
|
| Relations |
| BioSample |
SAMN09936788 |
| SRA |
SRX4624432 |
