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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Mar 01, 2023 |
| Title |
A lncRNA identifies Irf8 enhancer element in negative feedback control of dendritic cell differentiation |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
Dendritic cells (DC) are professional antigen presenting cells that develop from multipotent progenitors (MPP) and DC committed common DC progenitors (CDP) and further differentiate into different subsets: classical DC type 1 and 2 (cDC1 and cDC2, respectively) and plasmacytoid DC (pDC). In this study MPP, CDP, cDC1, cDC2 and pDC were obtained in a two-step in vitro culture system according to Felker et al., J. Immunol. 185, 5326-5335, 2010. Briefly, mouse bone marrow cells were first amplified with a specific cytokine cocktail and then induced to differentiate into DC with Flt3 ligand. MPP, CDP, cDC1, cDC2 and pDC were obtained by FACS sorting as follows: MPP: Gr1- CD117hi CD135low/-; CDP: Gr1- CD117int CD135+ CD115+; cDC1: CD11c+ CD11blow/- XCR1+; cDC2: CD11c+ CD11b+ XCR1- and pDC: CD11c+ CD11b- B220+. FACS sorted cells were then subjected to Omni-ATAC-seq, nuclear-titrated (NuTi) Capture-C targeting Irf8 promoter, and RNA-seq analysis. ATAC-seq data of cDC1 and pDC are published (Li et al., Genome Biol. 20, 45, 2019; GSE118221). ATAC-seq data of MPP, CDP and cDC2, NuTi Capture-C and RNA-seq data of MPP, CDP, cDC1, cDC2 and pDC are published here. CD11c+ CD11b+ B220- cDC and CD11c+ CD11b- B220+ pDC were obtained by FACS sorting and subjected to ChIP-seq analysis of IRF8 and are published here.
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| Overall design |
ATAC-seq analysis of mouse multipotent progenitors (MPP) and DC committed common DC progenitors (CDP), classical dendritic cells type 1 and type 2 (cDC1 and cDC2, respectively) and plasmacytoid dendritic cells (pDC) was performed by Omni-ATAC-seq according to Corces et al., Nat. Methods. 14, 959-962, 2017 with minor modifications as described in Li et al., Genome Biol. 20, 45, 2019 (GSE118221). NuTi Capture-C analysis (MPP, CDP, cDC1, cDC2 and pDC) was performed with a protocol modified from Downes et al., Nat. Commun. 12, 1-15, 2021 and Downes et al., Nat. Protoc. 17, 445-475, 2022. Design of Irf8 promoter viewpoint was with the design tool Oligo (https://oligo.readthedocs.io/en/latest/index.html) and resulted in 2 oligonucleotide probes targeting Irf8 promoter. Oligonucleotide probes were positioned adjacent to the DpnII cut sites on a restriction fragment spanning the Irf8 promoter (chr8:123,259,948-123,260,530). RNA-seq analysis (MPP, CDP, cDC1, cDC2 and pDC) and ChIP-seq analysis (cDC and pDC) was done as described in Allhoff et al., Nucleic Acids Res. 44, e153, 2016 (GSE73143).
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| Web link |
https://elifesciences.org/articles/83342
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| Contributor(s) |
Xu H, Li Z, Kuo C, Götz K, Look T, Toledo MA, Seré K, Costa IG, Zenke M |
| Citation(s) |
36916882 |
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| Submission date |
Mar 15, 2022 |
| Last update date |
Mar 15, 2023 |
| Contact name |
Zhijian Li |
| E-mail(s) |
zhijian.li@rwth-aachen.de
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| Organization name |
RWTH Aachen University
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| Lab |
Institute for Computational Genomics
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| Street address |
Pauwelsstr. 19
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| City |
Aachen |
| State/province |
North Rhine-Westphal |
| ZIP/Postal code |
52062 |
| Country |
Germany |
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| Platforms (2) |
| GPL19057 |
Illumina NextSeq 500 (Mus musculus) |
| GPL21626 |
NextSeq 550 (Mus musculus) |
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| Samples (25)
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| Relations |
| BioProject |
PRJNA816333 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE198651_RAW.tar |
3.2 Gb |
(http)(custom) |
TAR (of BIGWIG, TDF) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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