|
| Status |
Public on Jun 07, 2023 |
| Title |
Group 3 innate lymphoid cell, aged gut DN ILC3s rep3, H3K4me3 |
| Sample type |
SRA |
| |
|
| Source name |
small intestine
|
| Organism |
Mus musculus |
| Characteristics |
tissue: small intestine
cell type: Group 3 innate lymphoid cell
chip antibody: H3K4me3 antibody (39016, Active Motif)
strain: C57BL/6
age: 18-months-old
|
| Growth protocol |
DMEM, 15% fetal bovine serum, 2mM glutamine, 1x penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Small intestinal ILC3s were sorted from siLP of aged and young mice. H3K4me3 Chip of three subsets of ILC3s were both performed on 100,000 cells with modifications according to the protocol of Hyperactive In-Situ ChIP Library Prep Kit for Illumina (TD 901, Vazyme)
Briefly, sorted CCR6+ ILC3s，NKp46+ ILC3s and DN ILC3s were washed with 500 μl of wash buffer containing 1× protease inhibitor cocktail (5056489001, Sigma-Aldrich). Cell pellets were resuspended in wash buffer. After two washes with binding buffer, Concanavalin A-coated magnetic beads were added and incubated at room temperature. Bead-bound cells were resuspended in 50 μl of antibody buffer.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
All raw sequence data were quality trimmed using fastp (version0.19.7)
Aligned to the mm10 mouse genome using Bowtie2 (version 2.3.5.1) with options' –local–very-sensitive-local–no-unal–nomixed–no-discordant–phred33 -I 10 -X 700'.
PCR duplicates were removed using Picard MarkDuplicates (version 2.25.0).
Peaks were called using MACS2 (version 2.2.7.1) with options 'q 0.05'. DeepTools2 software (version 3.5.1) was used to create the peaks density plot and heatmap graph.
Visualization of peak distribution along genomic regions of interested genes was performed with IGV.
Genomic annotation was assigned using ChIPSeeker (version 1.28.3). Promoters were defined as follows: within 3000bp around the transcriptional start site (TSS).
Assembly: mm10
Supplementary files format and content: bigWig (except for Input sample)
|
| |
|
| Submission date |
Aug 01, 2022 |
| Last update date |
Jun 07, 2023 |
| Contact name |
lie wang |
| E-mail(s) |
wanglie@zju.edu.cn
|
| Organization name |
zhejiang universiry
|
| Department |
immunology
|
| Street address |
Zijingang Campus, Zhejiang University，Yuhangtang Road 866
|
| City |
hangzhou |
| State/province |
zhejiang |
| ZIP/Postal code |
310058 |
| Country |
China |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE210194 |
Cxxc finger protein 1 maintains homeostasis and function of intestinal group 3 innate lymphoid cells with aging [H3K4me3] |
| GSE210195 |
Cxxc finger protein 1 maintains homeostasis and function of intestinal group 3 innate lymphoid cells with aging |
|
| Relations |
| BioSample |
SAMN30078526 |
| SRA |
SRX16749552 |
