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Sample GSM3519812 Query DataSets for GSM3519812
Status Public on Jun 05, 2019
Title atac_ILC2_rep2
Sample type SRA
 
Source name Peripheral blood
Organism Homo sapiens
Characteristics cell type: FACS-purified lymphocytes
markers: CRTH2+
Extracted molecule genomic DNA
Extraction protocol Lymphocyte fractions were obtained from peripheral blood samples (buffy coats) donated by anonymous healthy donors. Cells were FACS-sorted using specific antibodies and YFP as described in detail in the manuscript.
Nextera DNA library construction (as described in Buenrostro et al. Nature Methods 2013).
 
Library strategy ATAC-seq
Library source genomic
Library selection other
Instrument model Illumina HiSeq 2500
 
Data processing Reads were aligned using bowtie2 with default parameters. Paired alignments spanning more than 1000 bp were filtered from the alignments.
Sorted and indexed bam files were parsed to HOMER to creat tag directories without duplicates and bedgraphs for browser visualization.
MACS2 software was used to call peaks.
Genome_build: hg38
Supplementary_files_format_and_content: MACS2 peak calling files (.txt)
 
Submission date Dec 18, 2018
Last update date Jun 05, 2019
Contact name Ralph Stadhouders
E-mail(s) stadhoudersralph@gmail.com
Organization name Erasmus Medical Center
Department Pulmonary Medicine
Street address Dr. Molewaterplein 50
City Rotterdam
ZIP/Postal code 3015 GE
Country Netherlands
 
Platform ID GPL16791
Series (1)
GSE124054 KLRG1 and NKp46 expressing CD117+ human innate lymphoid cell precursors are biased to ILC2 and ILC3, respectively
Relations
BioSample SAMN10612211
SRA SRX5161268

Supplementary file Size Download File type/resource
GSM3519812_ILC2_rep2_I18-1426-02.rg.filtered_peaks.txt.gz 846.3 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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