|
| Status |
Public on Feb 15, 2019 |
| Title |
LN naïve: DP ATAC-seq Rep 1 |
| Sample type |
SRA |
| |
|
| Source name |
naïve CD8+ T cells
|
| Organism |
Homo sapiens |
| Characteristics |
passages: FACS purified cells
tissue: hepatic lymph node
cell type: naive CD8+ T cells
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ATAC-seq: ATAC-seq was performed as previously described with minor modifications (Buenrostro et al., Nature Methods, 2013). Fifty thousand cells from FACS or from cultur were pelleted at 550 x g and washed with 1 mL 1x PBS followed by lysis with 50 μL lysis buffer (10 mM Tris-HCl [pH 7.4], 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630). Accessible chromatin was tagmented with Tn5 transposase (FC-121-1030; Illumina) for 45-75 minutes depending on the cell-type in a 37°C waterbath.
ATAC-seq: Tagmented DNA was amplified for 12 cycles of PCR, purified, and the prepared libraries were paired-end sequenced (38bp+37bp).
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
NextSeq 550 |
| |
|
| Data processing |
ATAC-seq: Quality assessment of raw reads was achieved with FastQC and contaminants were removed using Trimgalore. Human (GRCh37) reference genome was downloaded from UCSC repository Reads and samples were subsequently aligned using Bowtie. De novo motif analysis was performed on the top and bottom 100 enhancers using Homer. The top/bottom 100 enhancers were also linked to genes based on proximity (<10kbp) in order to enable GO term enrichment analysis using the GSEA website and volcano plot visualization between CD69+ and CD69- CD8+ T cells. Visualization of ATAC-seq tracks (peaks) was conducted using Integrative genomics viewer (igv) version 2.3.93.
Genome_build: mm10
|
| |
|
| Submission date |
Feb 15, 2018 |
| Last update date |
Nov 14, 2019 |
| Contact name |
Marcus Buggert |
| E-mail(s) |
[email protected]
|
| Organization name |
Karolinska Institutet
|
| Department |
Microbiology
|
| Street address |
C2:94; Karolinska Universitetssjukhuset Huddinge
|
| City |
Stockholm |
| State/province |
PA |
| ZIP/Postal code |
141 86 |
| Country |
Sweden |
| |
|
| Platform ID |
GPL21697 |
| Series (1) |
| GSE110684 |
Identification and characterization of HIV-specific resident memory CD8+ T cells in human lymphoid tissue |
|
| Relations |
| BioSample |
SAMN08545550 |
| SRA |
SRX3703079 |
