|
| Status |
Public on Jun 30, 2023 |
| Title |
scATAC-Seq Day 10 WT OT-I |
| Sample type |
SRA |
| |
|
| Source name |
Splenocytes
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Splenocytes
cell type: CD8 T cells
genotype: WT, OT-I
treatment: LM-actA-OVA
treatment: Day 10 post-infection
|
| Treatment protocol |
Please reference treatment protocol
|
| Growth protocol |
OT-I transgenic CD8 T cells expressing the congenic CD45.1 surface marker were expandedinvivowith listeria-actA-Ova. These cells were isolated from splenocytes at the indicated time points using FACS to collect CD45.1 expressing cells.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
For isolation of CD8 T cells 10 and 35 days after infection, single-cell suspensions were generated from four mice per recipient group by grinding spleens through nylon filters. CD8 T cells were enriched from these suspensions using Stemcell’s EasySep™ Mouse CD8 T Cell Isolation Kit (#19853). These samples were FcR blocked then stained with antibodies and live/dead stain (LIVE/DEAD™ Fixable Violet Dead Cell Stain Kit, # L34955) for 30 minutes on ice shielded from light. The antibodies used for cell surface staining from BioLegend were as follows; PE anti-mouse CD8b Antibody (YTS156.7.7) and APC anti-mouse CD45.1 Antibody (A20). Samples were subsequently washed twice and ~1X10^6 congenically marked OT-I cells were purified using fluorescence activated cell sorting for each group of recipients. The samples purified in this way from each group of recipients were then suspended in 100μL buffer and labeled with 1μg of Total-seq A antibodies (Biologend) per sample. DNA tagmentation and single cell capture and barcoding were performed using the 10x Genomics Single Cell ATAC v1 chemistry according to manufacturer's instructions.
Libraries from single cell-barcoded ATAC fragements were constructed using the 10x Genomics Single Cell ATAC v1 chemistry according to manufacturer's instructions.
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Barcode processing, demultiplexing, read mapping, peak calling and counting were performed using Cell Ranger ATAC (v.1.1.0) pipelines "mkfastq" and "count" using default parameters
Assembly: hg38 for human samples and mm10 for mouse samples
Supplementary files format and content: Barcode matrices in HDF5 format, fragments in tsv format, single cell metadata in csv format
|
| |
|
| Submission date |
Jun 09, 2023 |
| Last update date |
Jun 30, 2023 |
| Contact name |
Edward Usherwood |
| E-mail(s) |
d1261h4@dartmouth.edu
|
| Phone |
16036465224
|
| Organization name |
Geisel School of Medicine at Dartmouth College
|
| Department |
Microbiology and Immunology
|
| Street address |
Rubin Building, Level 7, 710-53
|
| City |
Lebanon |
| State/province |
NH |
| ZIP/Postal code |
03756 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE234574 |
Characterizing control of memory CD8 T cell differentiation by BTB-ZF transcription factor Zbtb20 using single cell RNA-sequencing (scATAC-Seq) |
| GSE234576 |
Characterizing control of memory CD8 T cell differentiation by BTB-ZF transcription factor Zbtb20 using single cell RNA-sequencing |
|
| Relations |
| BioSample |
SAMN35686926 |
| SRA |
SRX20647778 |
