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Sample GSM4413492 Query DataSets for GSM4413492
Status Public on Jul 28, 2020
Title AD_67_manual_H3K4me3
Sample type SRA
 
Source name S2 cells
Organism Drosophila melanogaster
Characteristics cell line: S2
chip ab: H3K4me3 (Diagenode, C15410003, lot A5051-001P)
Treatment protocol No treatment was applied
Growth protocol S2 cells were cultured in Express Five SFM (Thermo Fisher Scientific) supplemented with glutamax, at 27 °C. HepG2 liver hepatocellular carcinoma (ATCC, HB-8065TM) were cultured in Eagle’s minimal essential medium (EMEM, Lonza, 06-174) supplemented with 10% fetal bovine serum (Sigma), 2 mM L-glutamine (Lonza), 1.8 mM CaCl2, 1 mM sodium pyruvate (Lonza) and penicillin–streptomycin mixture (100 units/mL, Lonza), at 37 °C at 5% CO2 in 10 cm plates, up to 70%-80% confluency.
Extracted molecule genomic DNA
Extraction protocol HepG2 and S2 cells were fixed in 1% methanol-free formaldehyde (Thermo Scientific, 28906) in D-MEM (for HepG2 cells) or Express Five SFM (for S2 cells) for 15 min at room temperature under gentle shaking. Formaldehyde was quenched for 5 min by adding 125 mM glycine final concentration. Cells were rinsed twice with ice-cold PBS, harvested by scraping (HepG2) and pelleted (300 g, 10 min, 4 °C). Cells were processed according to RELACS / AutoRELACS protocols
Libraries were prepared according to Illumina's instructions using NebNext Ultra II kit. After Illumina adapter ligation, library was PCR amplified. Fragments were size-selected to eliminate adapter dimers contamination using AMPure XP beads. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on NovaSeq 6000 machine, following manufacturer's protocol.
High-throughput RELACS ChIP-seq and automated high-throughput AutoRELACS ChIP-seq
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina NovaSeq 6000
 
Data processing fastq files were demultiplexed on RELACS barcodes and aligned to dm6 (S2 cells) or hg38 (HepG2) using snakePipes v. 1.2.3. QC metrics and further downstream files (bigwig) were also generated using snakePipes (Bhardwaj et al. 2019)
default parameters used for the analysis are available at https://github.com/FrancescoFerrari88/AutoRELACS/tree/master/snakePipes_defaults
Genome_build: dm6 (S2 cells) and hg38 (HepG2)
Supplementary_files_format_and_content: bigWig, normalized coverage
 
Submission date Mar 16, 2020
Last update date Jul 29, 2020
Contact name Thomas Manke
E-mail(s) manke@ie-freiburg.mpg.de
Organization name Max Planck Institute of Immunobiology and Epigenetics
Street address Stuebeweg 51
City Freiburg
ZIP/Postal code 79108
Country Germany
 
Platform ID GPL25244
Series (1)
GSE147042 AutoRELACS: Automated Generation And Analysis of Ultra-parallel ChIP-seq
Relations
BioSample SAMN14383516
SRA SRX7917498

Supplementary file Size Download File type/resource
GSM4413492_AD_67_manual_H3K4me3.filtered.seq_depth_norm.bw 5.4 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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