|
| Status |
Public on Sep 13, 2019 |
| Title |
H3K27ac NKp46+ ILC3 Maf fl/fl Il7rCre Rep 2 |
| Sample type |
SRA |
| |
|
| Source name |
H3K27ac Maf KO
|
| Organism |
Mus musculus |
| Characteristics |
strain background: C57Bl/6 (N5 backcross)
genotype/variation: Maf fl/fl Il7r-Cre
age: adult
tissue: small intestine lamina propria
cell type: NKp46+ ILC3
|
| Growth protocol |
Mice were maintained under specific pathogen-free conditions.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Approximately 13 thousand NKp46+ ILC3s (CD3-CD19-CD127+CD90hiKLRG1-CCR6-NKp46+) were sort purified from the small intestine lamina propria of pooled adult Maf+/+ Il7rCre and Maf fl/fl Il7rCre. The CUT&RUN protocol was performed as previously described (Skene et al., 2018).
As described in Skene et al., 2018 using the KAPA HyperPrep Kit.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Nkp46_ILC3.cutandrun.H3K27ac.Maf_KO.rep2
|
| Data processing |
library strategy: CUT&RUN
Sequences for TruSeq Illumina adapters were removed from the raw reads using Trimmomatic v0.32 (Bolger et al., 2014).
Paired-end reads were mapped using Bowtie2 (v2.3.4.3 PMID: 22388286) against both Saccharomyces Cerevisiae (sacCer3) and Mouse (mm10) genomes in --very-sensitive-local mode, allowing for fragments of up to 700bp and discarding all but paired concordant alignments (parameters for bowtie2: -I 10 -X 700 --local --very-sensitive-local --no-discordant --no-mixed --no-unal --phred33).
Duplicates were removed using Picard MarkDuplicates v1.130
Signal files were generated with deeptools bamCoverage (v3.0.1 PMID:24799436) ignoring duplicates, extending reads to match the fragment size defined by paired mates and scaling the values by 1e6 divided by the total number of reads mapping against sacCer3 (parameters: --extendReads --ignoreDuplicates –scaleFactor 1e6/sacCer3_TOTAL_NREADS)
To quantify histone signal over specific genomic regions, featureCounts was used assigning fully aligned fragment counts toregions (parameters -p -B).
Genome_build: mm10
Supplementary_files_format_and_content: bigWig signal in RPMs
|
| |
|
| Submission date |
Sep 12, 2019 |
| Last update date |
Sep 13, 2019 |
| Contact name |
Maria Ciofani |
| E-mail(s) |
maria.ciofani@duke.edu
|
| Organization name |
Duke University School of Medicine
|
| Department |
Integrative Immunobiology
|
| Street address |
207 Research Drive, 128 Jones Building
|
| City |
Durham |
| State/province |
NC |
| ZIP/Postal code |
27710 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE137320 |
c-Maf regulates the plasticity of group 3 innate lymphoid cells by restraining the type 1 program [CUT&RUN] |
| GSE137322 |
c-Maf regulates the plasticity of group 3 innate lymphoid cells by restraining the type 1 program |
|
| Relations |
| BioSample |
SAMN12736175 |
| SRA |
SRX6835344 |
