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Sample GSM1861010 Query DataSets for GSM1861010
Status Public on Oct 30, 2015
Title H3K4me1 ChIP-seq from BN369 P1 cells
Sample type SRA
Source name in vitro differentiated plasmablasts
Organism Homo sapiens
Characteristics cell type: plasmablasts
origin: differentiation of NBC from buffy coat (healthy donor)
Growth protocol Naive B cells from healthy donors were purified by negative selection using magnetic cell separation (Miltenyi Biotech) and cultured at 7.5.105 cells/ml with the stimulation cocktail 1 (2,6 µg/ml Fab'2 anti-Ig, 100 ng/ml CD40 Ligand, 1 µg/ml CpG ODN 2006 and 50 U/ml IL2) for 4 days. Activated B cells were then washed and further cultured at 4.105 cells/ml with the differentiation cocktail 2 (50 U/ml IL2, 5 ng/ml IL4, 10 ng/ml IL10)
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was extracted using the AllPrep DNA/RNA mini kit (Qiagen) after cell-sorting (FACS Aria, BD) of blood or lymph node naive B cells and of in vitro differentiated plasmablasts (day 6 of the culture). For ChIP experiments, cells were fixed with 1% formaldehyde prior to cell sorting.
Genomic DNA (7 μg) from naïve B cells and plasmablasts was fragmented to 200 to 500 bp by sonication (Bioruptor, Diagenode) before incubation with β-glucosyltransferase and azide-glucose. Glucosylated 5hmCs were then labeled with biotin before enrichment of the biotinylated DNA fragments with streptavidin-coated magnetic beads. All steps used reagents from the Hydroxymethyl Collector kit (Active Motif). After elution from the beads, purified DNA was precipitated and processed for sequencing on a Highseq2000 (Illumina). Library preparations and sequencing reactions were run at the IGBMC genomic platform (Strasbourg, France). ChIP-seq was performed in P1 cells as follows. Cells were fixed for 8 minutes in 1% formaldehyde at room temperature and chromatin was sonicated for 15 minutes with the Bioruptor Sonication System (Diagenode). Immunoprecipitation was carried out with antibodies from Diagenode against H3K4me1 (pAb-194-050, lot: A1863-001P) and H3K27ac (pAb-196-050, lot: A1723-0041D) using approximately 500,000 cells per antibody. ChIP-seq libraries were constructed using the Kapa Hyper Prep Kit (Kapa Biosystems) and sequenced with an Illumina HiSeq1500 sequencer.
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 1500
Data processing SCL-seq fastq files were mapped to human hg19 genome assembly using Bowtie with parameters l=32 bp, n=1, m=1, strata, best, and Samtools.
The bam files were then processed to generate .wig files using MACS 1.4.0.
Genome_build: hg19
Supplementary_files_format_and_content: wig files
Submission date Aug 25, 2015
Last update date May 15, 2019
Contact name Gilles Salbert
Phone +33 223 236 625
Organization name University of Rennes 1
Department Biology
Lab UMR6290 CNRS
Street address Avenue du Général Leclerc
City Rennes
ZIP/Postal code 35042
Country France
Platform ID GPL18460
Series (2)
GSE72360 Mapping of 5-hydroxymethylcytosine by selective chemical labeling (SCL-seq) in human naive B cells and in vitro differentiated plasmablasts (P1 cells) [HTS]
GSE72498 Cell cycle-dependent reconfiguration of the DNA (hydroxy) methylome during terminal differentiation of human B cells into plasma cells
BioSample SAMN04011595
SRA SRX1164306

Supplementary file Size Download File type/resource
GSM1861010_BN369_H3K4me1_P1_cells.wig.gz 557.4 Mb (ftp)(http) WIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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