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AID-ChIP-seq Analysis of diffuse large B-cell lymphoma

ABSTRACT: AID-ChIP-seq Analysis of diffuse large B-cell lymphoma

PROVIDER: PRJNA611628 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR11278108_1.fastq.gz	Fastqsanger.gz
	SRR11278108_2.fastq.gz	Fastqsanger.gz
	SRR11278109_1.fastq.gz	Fastqsanger.gz
	SRR11278109_2.fastq.gz	Fastqsanger.gz
	SRR11278110_1.fastq.gz	Fastqsanger.gz

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AID Orchestrates MYC/E2F Target Gene Activation and Cell-of-Origin Transcriptional Programs in Diffuse Large B-cell Lymphoma [ABC_AID_KO_RNA-seq]

Project description:Activation-induced cytidine deaminase (AID), which is essential for antibody diversification, exhibits elevated expression in the activated B-cell-like (ABC) subtype of diffuse large B-cell lymphoma (DLBCL). Here, we demonstrate that AID modulates transcriptional programs linked to cell cycle progression, proliferation, and DLBCL subtype identity. AID loss in ABC-type DLBCL cell lines impairs MYC and E2F pathway activity, while AID re-expression restores activity, establishing a causal link. Furthermore, AID expression correlates with ABC-type stratification gene expression.

2026-03-01 | GSE308037 | GEO

AID-ChIP-seq Analysis of diffuse large B-cell lymphoma

Project description:Purpose: The goals of this study are to identify AID targets in DLBCL and investigate the overlapping of AID peaks and predicted G4 forming sequences (PQS) and the B-cell super enhancer (SE) U2932 DLBCL cells obtained from the American Type Culture Collection were grown in RPMI 1640 medium (Corning) supplemented with 10% FBS (Atlanta Biiologicals) and 1% Pen/Strep (Gibco). For each immunoprecipitation reaction, 4x106 chromatin cell equivalent were incubated overnight with either an AID antibody (Abcam, ab59361) or a rabbit IgG negative control antibody, subjected to protein A/G magnetic bead binding, IP elution and DNA recovery. The ChIP DNA was used to generate ChIPseq libraries with the ChIP-Seq sample preparation kit (Illumina) for sequencing at the Arkansas Children’s Research Institute Genomics Core. The sequence reads that passed quality filters were aligned to the human genome (hg19) using BWA-MEM and peakcalled using MACS2. Results: Using an optimized data analysis workflow, we mapped about 10-20 million sequence reads per sample to the human genome (build hg19) and identified 4,573 AID peaks which were filtered out if they overlap with the mock pull-down peaks and the blacklist (ENCODE blacklisted regions). We observed the intersection of AID peaks with PQS and SEs are significantly higher than expected by chance in all cases of comparisons supporting that the number of AID peaks sharing PQS and/or SEs is not a random event. Conclusions: Sequencing analyses reveal AID targets in both activated B-cells and lymphoma are highly enriched for G4 elements and validation studies confirm a representative set of these sequences form characteristic, stable G4 structures.

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AID Orchestrates MYC/E2F Target Gene Activation and Cell-of-Origin Transcriptional Programs in Diffuse Large B-cell Lymphoma [GCB_AID-ER_RNA-seq]

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AID Orchestrates MYC/E2F Target Gene Activation and Cell-of-Origin Transcriptional Programs in Diffuse Large B-cell Lymphoma [ABC_AID-ER_RNA-seq]

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Chip-chip from human diffuse large B cell lymphoma cell lines with IRF8

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Chip-chip from mouse diffuse large B cell lymphoma cell lines with IRF8

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Chip-chip from human diffuse large B cell lymphoma cell lines with IRF8

Project description:IRF8, a transcriptional factor, has the heightened expression in germinal center(GC) B cell and GC-origin B cell lymphoma. To identify IRF8 direct targets in GC B cells, ChIP-chip ananlysis was done in three different GC-origin diffuse large B cell lymphoma cell lines. IRF8-negative cell lines, MMS1, was also used as a negatvie control. IRF8 ChIP in three different cell lines (ODH1, VAL and LY1:high level of IRF8) and in one negative control cell lines (MMS1:negatvie for IRF8). Total four different samples. One sample per a set of two arrays (promoter1 and promoter2).

2011-10-14 | E-GEOD-30357 | biostudies-arrayexpress

Chip-chip from mouse diffuse large B cell lymphoma cell lines with IRF8

Project description:IRF8, a transcriptional factor, has the heightened expression in germinal center(GC) B cell and GC-origin B cell lymphoma. To identify IRF8 direct targets in GC B cells, ChIP-chip ananlysis was done in three different GC-origin diffuse large B cell lymphoma cell lines. IRF8-negative cell lines, MPC11, was also used as a negatvie control. IRF8 ChIP in three different cell lines (NFS201, NFS202 and NFS205:high level of IRF8) and in one negative control cell lines(MPC11:negatvie for IRF8). Total four different samples. One sample per a set of two arrays (promoter1 and promoter2).

2011-10-14 | E-GEOD-30519 | biostudies-arrayexpress

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