|
| Status |
Public on Aug 24, 2022 |
| Title |
TX1242_5_ATAC |
| Sample type |
SRA |
| |
|
| Source name |
peripheral B lymphocytes
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: PBMC-derived B cells
donor: TX1242 (donor 2)
infection: 5 days post EBV infection
|
| Treatment protocol |
Infection with B95-8 strain of EBV for 1 hr @ MOI of 5 (37°C, 5% CO2) [except for uninfected samples at Day 0]
|
| Growth protocol |
Culture in R15 media (RPMI1640 + 15% Heat-inactivated FBS + Pen/Strep/Glutamine + Cyclosporine A) @ 37°C, 5% CO2
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
10x Genomics scATAC + Gene Expression kit (single-cell mRNA and Tn5-accessible chromatin fragment capture)
10x Genomics scATAC + Gene Expression kit
Single-end gene expression libraries @ target of 50k reads per cell ; paired-end ATAC fragment libraries @ target of 50k total reads per cell (25k + / 25k - )
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Sample 7A
Single-cell chromatin accessibility (split across 2 flow cell lanes -- L001 / L002)
|
| Data processing |
Base-calling (cellranger-arc mkfastq; wrapper of Illumina bcl2fastq function for multiome samples)
Alignment (cellranger-arc count; tabulates cell-matched transcript counts and Tn5 insertion sites)
Filtering (cellranger-arc count -- default QC parameters for read filtering)
Peak-calling (ATAC) -- MACS2 / MACS3
Normalized abundance measurement (GEX) -- Seurat / Signac
Genome_build: hg38 ; hg38 + type 1 EBV (NC_007605)
Supplementary_files_format_and_content: count matrices (gene expression) and ATAC fragments (chromatin accessibility)
|
| |
|
| Submission date |
Nov 18, 2021 |
| Last update date |
Aug 25, 2022 |
| Contact name |
Elliott Daniel SoRelle |
| E-mail(s) |
elliott.sorelle@duke.edu
|
| Organization name |
Duke University
|
| Department |
Molecular Genetics & Microbiology
|
| Lab |
Micah Luftig Lab
|
| Street address |
130 Research Drive (CARL Building)
|
| City |
Durham |
| State/province |
NC |
| ZIP/Postal code |
27710 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE189141 |
Fate-resolved gene regulatory signatures of individual B lymphocytes in the early stages of Epstein-Barr Virus infection |
|
| Relations |
| BioSample |
SAMN23284974 |
| SRA |
SRX13167315 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5695155_TX1242_5_ATAC_EBV_atac_cut_sites.bigwig |
1.3 Gb |
(ftp)(http) |
BIGWIG |
| GSM5695155_TX1242_5_ATAC_EBV_atac_fragments.tsv.gz |
2.2 Gb |
(ftp)(http) |
TSV |
| GSM5695155_TX1242_5_ATAC_EBV_atac_peak_annotation.tsv.gz |
2.3 Mb |
(ftp)(http) |
TSV |
| GSM5695155_TX1242_5_ATAC_EBV_atac_peaks.bed.gz |
1.2 Mb |
(ftp)(http) |
BED |
| GSM5695155_TX1242_5_ATAC_atac_cut_sites.bigwig |
1.3 Gb |
(ftp)(http) |
BIGWIG |
| GSM5695155_TX1242_5_ATAC_atac_fragments.tsv.gz |
2.2 Gb |
(ftp)(http) |
TSV |
| GSM5695155_TX1242_5_ATAC_atac_peak_annotation.tsv.gz |
2.3 Mb |
(ftp)(http) |
TSV |
| GSM5695155_TX1242_5_ATAC_atac_peaks.bed.gz |
1.3 Mb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
