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Transcriptional profiles of knockouts of m6A writer and readers in Germinal Center B cells

ABSTRACT: Transcriptional profiles of knockouts of m6A writer and readers in Germinal Center B cells

PROVIDER: PRJNA747983 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR15188500_1.fastq.gz	Fastqsanger.gz
	SRR15188500_2.fastq.gz	Fastqsanger.gz
	SRR15188501_1.fastq.gz	Fastqsanger.gz
	SRR15188501_2.fastq.gz	Fastqsanger.gz
	SRR15188502_1.fastq.gz	Fastqsanger.gz

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Transcriptional profiles of knockouts of m6A writer and readers in Germinal Center B cells

Project description:We performed RNA-seq (MARS-seq) on germinal center (GC) light zone and dark zone B cells sorted to purity from freshly dissociated mouse popliteal lymph nodes immunized with NP-KLH for 7 to 14 days. Germinal center B cell subsets were gated as follows: Dump (CD8, CD4, F4/80, Gr-1)- B220+ CD38- GL-7+ FAS+. Dark zone GC cells were in addition CD86lo, CXCR4hi; LZ cells were in addition CD86hi, CXCR4lo. Three different mouse models were used: AID-cre Mettl3-flox, AID-cre Ythdf2-flox, Igf2bp3-knockout. We used these data to derive differentially expressed genes between B cell subsets of control and knockout genotypes. We also performed m6A-IP on ex vivo activated wild type B cells and determined the m6A targets in B cells. These studies revealed that the GC response depends on m6A RNA methylation and the functions of specific methyl-readers Ythdf2 and Igf2bp3.

2021-07-21 | GSE180359 | GEO

Proteome profiling of mouse germinal center B cells

Project description:Productive B cell responses are critical to protect a host from infection. The spleen and lymph nodes are populated by resting follicular B cells, which can enter germinal centers upon antigen encounter. Once in the germinal center, B cells migrate between the dark and light zones, where they undergo somatic hypermutation and selection, respectively. While germinal center B cells have been studied, an intense molecular understanding of these cells/subsets (and the differences between them) is lacking.

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ChIPseq analyses in germinal center B cells

Project description:Germinal center B cells were isolated from human tonsil tissue and crosslinked. ChIP was performed on two distinct pools of germinal center cells, each obtained from 3-5 donors. The experiment includes two biological replicates (germinal center cell pools from different donors). ChIP was performed on both pools and subject to library preparation and sequencing. Input DNA was sequenced for both pools.

2015-12-04 | E-GEOD-68349 | biostudies-arrayexpress

Deletion of miR-15a/16-1 in murine germinal center B-cells.

Project description:Given the tumor suppressing function of miR-15a/16-1 cluster, we studied its role in the germinal center B-cells that give rise to most lymphoid malignancies.

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AI-empowered integrative structural characterization of m6A writer complex

Project description:Investigation into the structure of the human m6A writer complex.

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Ythdf m6A readers compensate each other in a context dependent manner [eCLIP]

Project description:YTH domain family proteins Ythdf1, Ythdf2, Ythdf3 are three readers with highly similar structure, which were shown to have different roles in the cell. However, their similarity and the fact that they tend to bind the same targets suggest that in some cases they may have an overlapping role. In this paper, we systematically knocked-out (KO) each of the three readers and the three together (triple-KO), and estimated the effect in-vitro in mouse embryonic stem cells (mESCs), and in-vivo, in viability and gametogenesis. We show that in mESCs there is a compensation between the three readers, with a dramatic hyper-pluripotent phenotype only in the triple-KO. However, in-vivo, Ythdf2 has a dominant role that cannot be compensated by Ythdf1 or Ythdf3, both in viability of the mouse pups and in gametogenesis. We suggest that compensation is dosage-dependent, and in-vivo we cannot detect it due to difference in the readers’ expression, both in level and in spatial location. In addition, we found that Ythdf1 and Ythdf3 specifically down-regulate 2-cell genes, that Ythdf2-KO in gametogenesis affects microtubuline related genes, and that Mettl3-KO severity is increased as the deletion occurs earlier in gametogenesis.

2020-06-04 | GSE151788 | GEO

ChIPseq analyses in germinal center B cells

2015-12-04 | GSE68349 | GEO

Ythdf m6A readers compensate each other in a context dependent manner [Ribo-seq]

2020-06-04 | GSE148536 | GEO

Ythdf m6A readers compensate each other in a context dependent manner [RNA-seq]

2020-06-04 | GSE147849 | GEO

Gene Expression Profiles of Germinal Center B Cells

Project description:We report the gene expression profiles of germinal center B cells obtained by FACS analyses of normal human lymph nodes. We used FACS analyses to isolate germinal center B cells from 3 different individuals with one individual sampled twice. The overall goal was simply to identify genes that are highly expressed or silent in these purified cell populations.

2009-07-31 | E-GEOD-16712 | biostudies-arrayexpress

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