|
| Status |
Public on Jun 15, 2020 |
| Title |
ART Patient 03 RNAseq Naive CD4 T cells |
| Sample type |
SRA |
| |
|
| Source name |
Naive CD4 T cells
|
| Organism |
Homo sapiens |
| Characteristics |
patient: ART Patient 03
tissue: peripheral blood
replicate: 1
cell type: Naive CD4 T cells
|
| Treatment protocol |
There is no treatment for patient samples.
|
| Growth protocol |
Ex vivo PBMC from different patient cohorts were directed sorted and used for NGS.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using a commercial PicoPure RNA Isolation Kit
Whole transcriptome amplification (WTA) and tagmentation-based library preparation was performed using SMART-seq2, followed by sequencing with a 75-cycle kit on a NextSeq 550 instrument (Illumina, CA). The quantification of transcript abundance was conducted using RSEM software (v1.2.22) supported by the STAR aligner software (STAR_2.4.2a). The raw reads were aligned to the GRCh38 human genome database.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 550 |
| |
|
| Description |
CJ-ART-13
|
| Data processing |
FASTQ files were obtained by Illumina demultiplexing pipeline. STAR and RSEM were used to align to GRCh38 and to calculate the raw counts for genes, respectively.
Genome_build: GRCh38
Supplementary_files_format_and_content: raw counts and TPM in csv, summits in BED
|
| |
|
| Submission date |
Jan 27, 2020 |
| Last update date |
Jun 15, 2020 |
| Contact name |
Ce Gao |
| E-mail(s) |
CGAO4@MGH.HARVARD.EDU
|
| Organization name |
Ragon Institute of MGH, MIT and Harvard
|
| Lab |
Yu/Lichterfeld Labs
|
| Street address |
400 Technology Square
|
| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02139 |
| Country |
USA |
| |
|
| Platform ID |
GPL21697 |
| Series (2) |
| GSE144332 |
A unique viral reservoir landscape associated with durable natural control of HIV-1 infection [RNA-seq] |
| GSE144334 |
A unique viral reservoir landscape associated with durable natural control of HIV-1 infection |
|
| Relations |
| BioSample |
SAMN13930468 |
| SRA |
SRX7637945 |
