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Sample GSM1869149 Query DataSets for GSM1869149
Status Public on May 13, 2016
Title BJELM_H3K27me3_ChIP-seq
Sample type SRA
Source name Transformed BJELM fibroblast cells (cancer cells)
Organism Homo sapiens
Characteristics cell line: BJELM
cell type: foreskin fibroblast cells
chip antibody: anti-H3K27me3
chip antibody supplier: millipore
chip antibody catalog#: 07-449
chip antibody lot #: 2039786
Growth protocol BJELM cells were cultured in monolayer conditions Dulbecco’s modified Eagle’s medium (DMEM)/M199 (4:1) (with 4.5 g/l glucose) supplemented with 10% of heat inactivated fetal calf serum (FCS),G-418 (400 µg/µl), Hygromycin (400 µg/µl) and puromycin (1 µg/ml) and continuously grown with 10-6 M 4-hydroxytamoxyfen (4-OHT).
Extracted molecule genomic DNA
Extraction protocol cells were fixed with 1% para-formaldehyde (Electron Microscopy Sciences) for 30 minutes at room temperature. ChIP assays were performed following previously described conditions: chromatin sonication and immunoprecipitation in lysis buffer (50mM Tris–HCl pH=8, 140mM NaCl, 1mM EDTA, 1% Triton, 0.1% Na-deoxycholate) complemented with protease inhibitor cocktail (Roche 11873580001); 2x washes with lysis buffer; 2x washes with lysis buffer containing 500mM NaCl; 2x washes with washing buffer (10mM Tris–HCl pH=8, 250mM LiCl, 0.5% NP-40, 1mM EDTA, 0.5% Na-deoxycholate); 2x washes with 1x TE buffer; elution at 65°1C; 15 min at 65°C in elution buffer (50mM Tris–HCl pH=8, 10mM EDTA, 1% SDS); overnight decrosslinking at 65C followed by PCI purification. qPCR-qualified ChIP assays were quantified (Qubit dsDNA HS assay kit; Invitrogen); 10 ng of the ChIPed material was used for preparing Illumina sequencing libraries.
Libraries were prepared following a multiplexing approach (NEXTflexTM ChIP-seq Bioo Scientific kit; ref: 5143-02).
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2000
Description Transformed BJELM fibroblast cells (cancer cells)
ChIP against H3K27me3
Data processing Prepared sequencing libraries were sequenced on the Illumina instrument HiSeq2000. Regular Illumina pipelines were used for image processing and base calling.
bed files obtained from the aligned profiles using peak calling tools MeDiChi-seq (for RNA PolII and H3K9ac, H3K4me3, H3K27ac marks) ann SICER tool (for H3K27me3) with the input datasets as a negative control
Genome_build: hg19
Supplementary_files_format_and_content: wig and bed (peak annotation information)
Submission date Sep 04, 2015
Last update date May 15, 2019
Contact name Valeriya Malysheva
Organization name IGBMC
Street address 1 rue Laurent Fries
City Illkirch; Strasbourg
ZIP/Postal code 67404
Country France
Platform ID GPL11154
Series (2)
GSE72532 Reconstructing gene regulatory networks of tumorigenesis [ChIP-Seq]
GSE72533 Reconstructing gene regulatory networks of tumorigenesis
BioSample SAMN04032802
SRA SRX1184136

Supplementary file Size Download File type/resource
GSM1869149_BJELM_H3K27me3_SICER.bed.gz 1.3 Mb (ftp)(http) BED
GSM1869149_BJELM_H3K27me3_merged_normalized.wig.gz 38.2 Mb (ftp)(http) WIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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