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Sample GSM4478803 Query DataSets for GSM4478803
Status Public on Dec 11, 2020
Title Nonmemory NK cells_Rep1
Sample type SRA
 
Source name Spleen
Organism Mus musculus
Characteristics strain: C57BL/6
cell type: CD27- NK cells
infection: Zika virus
Treatment protocol Naive, CD27+ and CD27- NK cells were FACS sorted and proceeded for tagmentation immediately as per standard protocol.
Growth protocol NK cells were harvested from mice spleen on day 37 post-infection.
Extracted molecule genomic DNA
Extraction protocol Intact nuclei were isolated after cell lysis, and tagmentation was performed using tagment DNA enzyme I (Illumina) and DNA was purified using Qiagen MinElute Reaction Cleanup Kit.
Standard ATACseq protocol from 50000 cells.
Paired-end 150 bp reads, Illumina HiseqX.
 
Library strategy ATAC-seq
Library source genomic
Library selection other
Instrument model HiSeq X Ten
 
Description CD27-_N_1
Chromatin
Data processing Reads were aligned to mouse genome (mm10) using BWA.
Peak calling was performed using Homer.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *_ATAC_Normalized_counts.txt: Tab-delimited text files include TMM normalized data.
 
Submission date Apr 16, 2020
Last update date Dec 11, 2020
Contact name Sachin Mulik
E-mail(s) sachin.mulik@uthct.edu
Phone 9038772826
Organization name The University of Texas Health Science Center at Tyler
Department Pulmonary Immunology
Street address 11937 US Hwy 271
City Tyler
State/province Texas
ZIP/Postal code 75708
Country USA
 
Platform ID GPL21273
Series (1)
GSE148780 Memory like NK cells display stem cell like properties after Zika virus infection
Relations
BioSample SAMN14605521
SRA SRX8123918

Supplementary file Size Download File type/resource
GSM4478803_N1_ATAC_Normalized_counts.txt.gz 530.1 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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