U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

SRX7795856: GSM4337243: DL135_H3AC_ChIP; Homo sapiens; ChIP-Seq
1 ILLUMINA (Illumina HiSeq 2000) run: 26.5M spots, 1.1G bases, 694.4Mb downloads

Submitted by: NCBI (GEO)
Study: Key Super Enhancers Drive Tumor-Suppressing Transcription Feedback Programs in Mature B Cell Cancers (ChIP-seq, FAIRE-seq)
show Abstracthide Abstract
Dynamic changes to the epigenome are essential regulators of B cell differentiation and, when perturbed, can lead to cancer. We compared three types of mature B cell lymphoma/leukemia (BCL) and normal lymphocytes to identify common and distinct epigenetic perturbations that promote oncogenesis. Purified malignant B cells from 52 patients (18 Follicular, 11 Diffuse Large B Cell, 23 Chronic Lymphocytic Lymphomas) and normal B cell subsets from 28 donor tonsils were subjected to chromatin immunoprecipitation and sequencing (ChIP-seq) for H3K4me1, H3K9/14ac, and H3K27ac; FAIRE-seq for open chromatin; RNA-seq; and genome copy number arrays. We identified a novel super enhancer (SE) connected to the aberrant expression of FCMR and PIGR in multiple BCL subtypes, which may drive the tissue-specific expression of the two immunoglobulin receptor genes. These integrative studies also revealed that loss of normal B cell SEs in BCL was associated with significant reduction in linked gene expression, the greatest impact among regulatory elements. Downregulation of crucial B cell transcription factors (TF) and tumor suppressors was consistent across BCL subtypes and linked to significantly diminished or absent active chromatin marks in adjacent SEs. These BCL-repressed SEs are enriched in binding sites for the same suppressed TFs that they regulate, suggesting transcriptional regulatory feedback loops for these key B cell identity genes. In sum, this study defined common alterations in the regulomes of mature B cell leukemias and lymphomas and implicate SEs as important hubs of tumor suppressing transcriptional feedback loops that are perturbed in B cell cancer. Overall design: 42 or 50 bp single-end ChIP-sequencing was performed on DNA libraries generated from sorted CD19+ B cells from primary peripherial blood or lymph node biopsies of chronic lymphocytic leukemia, follicular lymphoma, and diffuse large B cell patients or donor tonsils.
Sample: DL135_H3AC_ChIP
SAMN14175838 • SRS6211225 • All experiments • All runs
Organism: Homo sapiens
Library:
Instrument: Illumina HiSeq 2000
Strategy: ChIP-Seq
Source: GENOMIC
Selection: ChIP
Layout: SINGLE
Construction protocol: Cells were formaldehyde cross-linked (1% final concentration) for 10 minutes in RPMI with 10% FBS. Quenching was performed by addition of 1M glycine (125 mM final concentration) with gentle mixing for 10 minutes at room temperature. Cells were washed with cold PBS and lysed in an SDS buffer (1% SDS, 10 mM EDTA, 50 mM Tris pH 8.0) with protease inhibitors before chromatin was fragmented using a Diagenode Bioruptor to an average size of less than 300 bp as determined using an Agilent Bioanalyzer 2100. Lysates were immunoprecipitated with the listed antibodies conjugated to Protein-A Dynabeads (5 ug antibody incubated with beads for 2-4 hours at 4°C) overnight at 4°C. The beads were then washed with the following buffers each for 3 minutes at 4°C - low salt buffer (150 mM NaCl, 50 mM Tris pH 8.0, 0.1% SDS), high salt buffer (500 mM NaCl, 50 mM Tris pH 8.0, 0.1% SDS), LiCl buffer (250 mM LiCl, 50 mM Tris pH 8.0, 0.5% Na deoxycholate, 1% NP40), and TE buffer (10 mM Tris pH 8.0, 1 mM EDTA). After washing, crosslinks were reversed overnight at 65°C in 250 uL elution buffer (1% SDS, 100 mM NaHCO3) followed by addition of proteinaseK and incubation at 56°C for 1 hour. DNA was purified with QIAquick PCR purification columns. At least 3 ng of DNA was used to for indexed library preparation using Illumina TruSeq adapters and standard Illumina protocols. Fragments were size selected (average fragment-size: 200-400 bp for ChIP; 50-200 for FAIRE) using Agencourt AMPure XP beads prior to amplification. Samples were pooled (6-10 per lane) and sequenced.
Experiment attributes:
GEO Accession: GSM4337243
Links:
Runs: 1 run, 26.5M spots, 1.1G bases, 694.4Mb
Run# of Spots# of BasesSizePublished
SRR1117475326,541,8551.1G694.4Mb2021-09-03

ID:
10174084

Supplemental Content

Search details

See more...

Recent activity

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...