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Sample GSM2616171 Query DataSets for GSM2616171
Status Public on Mar 14, 2018
Title k4m2_ILC2_BAL1
Sample type SRA
 
Source name bronchoalveolar lavage (BAL)
Organism Mus musculus
Characteristics cell type: FACS-purified lymphocytes
antibody: anti-H3K4Me2, Abcam ab32356
Growth protocol Only for aILC2: 7 days of culture (no feeders) in Yssel's medium supplemented with IL-2, IL-7, IL-25 and IL-33. See Lim et al. Journal of Experimental Medicine (2016)
Extracted molecule genomic DNA
Extraction protocol Murine ILC2s were obtained from Gata3-YFP/YFP mice with airway inflammation, human ILC2s from peripheral blood. Cells were FACS-sorted using specific antibodies (and YFP for murine cells) as described in detail in the manuscript.
ChIPmentation: Nextera DNA library construction (as described in Schmidl et al. Nature Methods 2015); RNA-Seq: Smart-seq2library construction (as described in Picelli et al. Nature Methods (2013)
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina NextSeq 500
 
Data processing Reads were aligned using bowtie2 (ChIPmentation) or HISAT (RNA-seq) with default parameters.
Sorted and indexed bam files were parsed to HOMER to creat tag directories without duplicates and bedgraphs for browser visualization
ChIPmentation: HOMER was used to identify enriched regions ('peak calling') using findPeaks with -region -size 1000 -minDist 2500 options
RNA-seq: Sample scaling and statistical analysis were performed using the R package DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: HOMER peak calling (ChIPmentation) or RPKM expression values (RNA-Seq)
 
Submission date May 11, 2017
Last update date May 15, 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 GPL19057
Series (1)
GSE98843 Epigenome analysis reveals novel aspects of ILC2 activation and supports a pathogenic role in asthma
Relations
BioSample SAMN06933060
SRA SRX2802555

Supplementary file Size Download File type/resource
GSM2616171_ilc2b_k4m2_peaks.bed.gz 458.4 Kb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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