|
| Status |
Public on May 03, 2021 |
| Title |
k4me2_naiveT_2 |
| Sample type |
SRA |
| |
|
| Source name |
mediastinal lymph node
|
| Organism |
Mus musculus |
| Characteristics |
tissue: mediastinal lymph node
cell type: naive T cells
antibody: anti-H3K4Me2, Abcam ab32356
|
| Treatment protocol |
NA
|
| Growth protocol |
NA
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lymphocyte fractions were obtained from Gata3-YFP/YFP mice with airway inflammation. Cells were FACS-sorted using specific antibodies and YFP as described in detail in the manuscript.
Nextera DNA library construction (as described in Schmidl et al. Nature Methods 2015).
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
gnegm_k4m2
|
| Data processing |
Reads were aligned using bowtie 2with default parameters.
Sorted and indexed bam files were parsed to HOMER to creat tag directories without duplicates and bedgraphs for browser visualization.
HOMER was used to identify enriched regions ('peak calling') using findPeaks with -region -size 1000 -minDist 2500 options
Genome_build: mm10
Supplementary_files_format_and_content: HOMER peak calling files
|
| |
|
| Submission date |
Nov 29, 2016 |
| Last update date |
May 03, 2021 |
| 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) |
| GSE90641 |
Epigenome analyses implicate ILC2s as key mediators of allergic airway inflammation |
|
| Relations |
| BioSample |
SAMN06067821 |
| SRA |
SRX2380908 |
