|
| Status |
Public on Jun 15, 2020 |
| Title |
ART Patient 03 ATACseq Naive CD4 T cells (1) |
| 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 |
genomic DNA |
| Extraction protocol |
DNA was treated with Tn5 and purified using Chip dna clean & concentrator
20,000 sorted cells were centrifuged at 1500 rpm for 10 min at 4°C in a pre-cooled fixed-angle centrifuge. All supernatant was removed and a modified transposase mixture (including 25 µl of 2x TD buffer, 1.5 µl of TDE1, 0.5 µl of 1% digitonin, 16.5 µl of PBS, 6.5 µl of nuclease-free water) was added to the cells and incubated in a heat block at 37°C for 30 min. Transposed DNA was purified using a ChIP DNA Clean & Concentrator Kit (Zymo Research #D5205) and eluted DNA fragments were used to amplify libraries.
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
NextSeq 550 |
| |
|
| Data processing |
Reads were trimmed for adaptor sequence, then mapped to GRCh38 using bowtie2, duplicate fragments were then removed using Picard. Peaks were called using MACS2. For duplicated samples, peaks were merge using Bioconductor.
Genome_build: GRCh38
Supplementary_files_format_and_content: 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) |
| GSE144329 |
A unique viral reservoir landscape associated with durable natural control of HIV-1 infection [ATAC-seq] |
| GSE144334 |
A unique viral reservoir landscape associated with durable natural control of HIV-1 infection |
|
| Relations |
| BioSample |
SAMN13930346 |
| SRA |
SRX7637780 |
