|
| Status |
Public on Apr 20, 2024 |
| Title |
B6_Spleen_NK_Ly49C_and_Ly49I_neg_rep2_ATAC |
| Sample type |
SRA |
| |
|
| Source name |
Spleen
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6J
tissue: Spleen
cell line: primary cells
cell type: Natural killer cells
marker: CD3-CD19-NK1.1+NKp46+NKG2A-
subset: Ly49C_and_Ly49I_neg
genotype: WT
treatment: ex vivo
|
| Treatment protocol |
Splenic NK cells or CD8 Tregs were FACS-sorted from mice or rats
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was extracted according to a previously published protocol (Wu, J. et al. Requisite Chromatin Remodeling for Myeloid and Erythroid Lineage Differentiation from Erythromyeloid Progenitors. Cell Reports 33, 108395 (2020).)
libraries were constructed using a previously published protocol (Wu, J. et al. Requisite Chromatin Remodeling for Myeloid and Erythroid Lineage Differentiation from Erythromyeloid Progenitors. Cell Reports 33, 108395 (2020).)
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
instrument model: Element AVITI
|
| Data processing |
Mouse ATAC data were first processed using the AIAP (v1.1) pipeline. As a part of the pipeline: locations of Tn5 insertion events were inferred from properly paired, non-PCR duplicate reads with MAPQ >= 10; each Tn5 insertion event was extended from insertion site up and down 75 bp to generate a 150 bp “pseudo read”; pseudo reads were piled up to generate an ATAC signal profile, which was normalized against sequencing depth. The resulting normalized ATAC signal profile was used in genome browser views unless otherwise noted.
For Ly49 consensus views of mouse and rat ATAC data, we fine-tuned the alignment using a custom alignment pipeline (https://github.com/ChangxuFan/snakeATAC/): adaptors were removed using cutadapt (v1.18) with parameters “--quality-cutoff=15,10 --minimum-length=36”; reads were aligned to reference genomes using “bowtie2 --very-sensitive --xeq --dovetail --no-unal”; only reads with perfect match to the reference were kept (“sambamba view -f bam -F '[AS] == 0'”). This was applied because we aligned ATAC data against genomes assembled from exactly the same mouse/rat strains; when indicated, reads were filtered based on MAPQ (“sambamba view -f bam -F 'mapping_quality >= 8 '”); “methylQA48 atac -X 38 -Q 1 ” was used to remove PCR duplicates, identify Tn5 insertion sites, and generate smoothed ATAC signals through extending Tn5 insertion sites up and downstream 75 bp, similar to the AIAP package.
Assembly: B6 reads were aligned to mm10. Rat reads were aligned to rn7. 129 and NOD reads were aligned to custom-built genomes, which were detailed in the “Ly49 and genome sequences and annotations” method section in the manuscript, and available at https://github.com/ChangxuFan/Ly49evolution
Supplementary files format and content: bigwig: AIAPnorm.bw files are the normalized ATAC signals from the AIAP pipeline. unnorm.bw is the unnormalized ATAC signals from the snakeATAC pipeline (this study). MAPQ8 indicates that reads were filtered for MAPQ >= 8.
|
| |
|
| Submission date |
Feb 16, 2024 |
| Last update date |
Apr 20, 2024 |
| Contact name |
Changxu Fan |
| E-mail(s) |
fanc@wustl.edu
|
| Organization name |
Washington University in St. Louis
|
| Department |
Genetics
|
| Lab |
Ting Wang Lab
|
| Street address |
4515 McKinley Avenue, Room 5213
|
| City |
Saint Louis |
| State/province |
Missouri |
| ZIP/Postal code |
63110 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE226498 |
Epigenetic evolution of the Ly49 gene family [ATAC-Seq] |
| GSE226502 |
Epigenetic evolution of the Ly49 gene family |
|
| Relations |
| BioSample |
SAMN39969357 |
| SRA |
SRX23645934 |
