|
| Status |
Public on Oct 10, 2022 |
| Title |
P14 cells from TdLN (D21) 1 |
| Sample type |
SRA |
| |
|
| Source name |
Lymphocytes
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
time point: WT
genotype: D21
cell sorting stratergy: CD45.1+CD44+CD8 T cells
|
| Growth protocol |
We first subcutaneously engrafted C57L/B6 (B6) mice with half million of B16.F10 cells expressing the lymphocytic choriomeningitis virus (LCMV) glycoprotein (hereafter referred as B16.Gp) as a surrogate TSA to generate a mouse melanoma model. Then 5x105 CD44-GFP+ naïve P14 cells bearing transgenic TCR specific for H-2Db LCMV-GP33-41 epitope that were isolated from TCF-1-GFP reporter P14 mice were transferred into tumor-bearing mice at day 8 (D8) post B16.Gp inoculation. To define the molecular basis for memory-like CD8+ T cells in TdLN, we performed ATAC-seq on antigen specific CD8+ T cells originated from TdLNs of melanoma tumor model at indicated timepoints post P14 cell transfer.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Briefly, 50,000 target cells were washed with PBS and then treated with lysis buffer, followed by labeling with the Nextera enzyme according to standard Illumina protocols (15027865; Illumina).
The labeled samples were immediately amplified by 9–10 cycles of polymerase chain reaction (PCR) with barcoded primers and sequenced with a NovaSeq 6000 instrument in a 150 bp/150 bp paired-end run using standard Illumina protocols.
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
P14 cells from TdLN (D21)
|
| Data processing |
ATAC-seq reads were aligned to the mm10 genome assembly using bwa version 0.7.15 with “mem” algorithm
Mapped reads were filtered for mapping quality (-q 20), and duplicates were removed using MarkDuplicates tool in Picard
Peaks were called using MACS2 with the following setting: --call-summits --nomodel --shift -100 --extsize 200 –keep-dup all
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using deepTools version 2.0 with the following setting: --normalizeUsing RPKM.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files were generated using deepTools version 2.0
Supplementary_files_format_and_content: peak text files
|
| |
|
| Submission date |
Jul 14, 2021 |
| Last update date |
Oct 10, 2022 |
| Contact name |
lilin ye |
| E-mail(s) |
yelilinlcmv@tmmu.edu.cn
|
| Organization name |
Third Military Medical University
|
| Department |
Institute of Immunology
|
| Street address |
Gaotanyan Street, Shapingba District
|
| City |
Chongqing |
| ZIP/Postal code |
400038 |
| Country |
China |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE180084 |
ATAC-seq of antigen-specific CD8+ T cells from tumor draining LNs of melanoma bearing mice |
| GSE180095 |
Antigen-specific CD8+ T cells from tumor draining of melanoma bearing mice |
|
| Relations |
| BioSample |
SAMN20209015 |
| SRA |
SRX11439363 |
