|
| Status |
Public on Mar 14, 2018 |
| Title |
k4m2_ILC2_BAL2 |
| 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 |
SAMN06933074 |
| SRA |
SRX2802556 |
