2025-10-30
ENA first public
ERC000011
ENA-CHECKLIST
Department of Microbiology & Immunology, University of Maryland School of Medicine
INSDC center name
public
INSDC status
ERS27118087
SRA accession
E-MTAB-15786:ATACD101_S1
Submitter Id
ATAC-seq
assay type
ArrayExpress
broker name
Mixed immune cells
cell type
not collected
collection date
house mouse
common name
Protocols: Experimental protocols for ASAPseq data acquisition followed the following design: dissociated single cell suspensions from each mouse were dispensed into two sets of 96-well plates, with each well containing approximately 150,000 cells. Then cells were blocked with an anti-mouse CD16/32 antibody (Trustain FcX Plus: BioLegend) to prevent non-specific binding via the Fc receptor. After blocking, the cells were stained with Total Seq-B anti-mouse hashtag antibody (BioLegend). Hash-tagged cells were then pooled together (approx. 2 million cells) and stained with a mixture of sixty-two TotalSeq-B anti-mouse surface protein panel antibodies at concentrations ranging from 12.5ng to 100ng per pooled sample. Stained cells were washed with Cell Staining Buffer (BioLegend). Cell numbers were counted, along with viability. 5-week-old C57BL/6J mice were pre-exposed sequentially to Influenza A/Puerto Rico/8/34 (PR8) virus and Plasmodium yoelii strain 17XNL. Four doses of 1mg chloroquine were administered intraperitoneally over the course of 3 weeks to clear the malaria infection. Pre-exposed mice (now 12-15 weeks old) were injected intraperitoneally with 3mg anti-mouse IFNAR-1 to prevent rapid clearance of the vaccine’s virus by Type I interferon responses. One day later, mice were vaccinated subcutaneously in one caudal thigh muscle with live-attenuated virus yellow fever vaccine YF17D (Sanofi Pasteur) or the same vaccine inactivated with formalin.  Serum was removed from whole blood, after which red blood cells were lysed with Ack lysing buffer. Lymphocytes were isolated from all tissues using density gradient centrifugation. Cells were stained with CITE-seq antibodies (HTOs and ADTs), after which single cells were encapsulated in gel-beads-in-emulsion. 10x Genomics ATAC protocol (CG000496 Rev B).
description
not collected
geographic location (country and/or sea)
not applicable
isolate
Mus musculus
organism
Mus musculus
organism
Mus musculus
scientific_name
b6
strain
ATACD101_S1
title