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Sample GSM3900111 Query DataSets for GSM3900111
Status Public on Feb 01, 2021
Title ZC3H4-ChIPseq_LPS_45min_rep2
Sample type SRA
Source name Macrophages
Organism Mus musculus
Characteristics cell type: RAW 264.7 Macrophages
genotype: wild type
strain: BALB/c
chip antibody: anti-ZC3H4 (Sigma, HPA040934)
Treatment protocol Cells were treated for 45 minutes with LPS (10 ng/ml) before harvesting.
Growth protocol RAW 264.7 mouse macrophage cell line was purchased from the American Type Culture Collection (ATCC). Cells were grown in DMEM containing 10% South American FBS, 1% L-Glutamax solution and 1% Pen/Strep solution.
Extracted molecule genomic DNA
Extraction protocol Ca. 200 mill. cells were pelleted and resuspended in PBS and fixed first with disuccinimidyl glutarate at 2mM final concentration for for 45 min at room temperature, followed by 1% formaldehyde fixation for 10 min. Nuclear lysates were prepared, sonicated to reach an average fragment length of 300 bp, whereafter protein-DNA complexes were immunoprecipitated with specific antibodies.
DNA libraries were prepared for sequencing on the NextSeq as previously described (Ostuni, 2013).
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina NextSeq 500
Description Chromatin IP against ZC3H4
Data processing Single end reads (76bp) were trimmed and clipped for quality control with Trimmomatic v0.27 (PMID:24695404). Read quality was then checked for each sample using FastQC v0.10.1 ( High-quality reads were mapped using Bowtie2 v 2.2.6 (PMID: 19261174). We used default parameters with the options --very-sensitive, --no-unal and with the pre-built bowtie2 index. Only uniquely mapping reads were retained.
Peak calling was performed using SICER v2 (PMID: 24743992). We identified significantly enriched clusters using a redundancy threshold of 1, a window size of 200 bp, a gap size of 600 bp and a False Discovery Rate (FDR) cut-off <0.01 were used. and a False Discovery Rate (FDR) cut-off <0.01 were used Fragment size was set to 150nt and the effective genome fraction to 0.80. The ChIP was compared to input DNA derived from RAW264.7 mouse macrophages. Regions that overlapped with the blacklists of the ENCODE and modENCODE consortia ( were filtered out.
Tracks (*.bigWig files) were generated using bamCoverage from deepTools v.3.1.3 (PMID:27079975)
Genome_build: mm10 (GENCODE)
Supplementary_files_format_and_content: bigWig
Submission date Jun 20, 2019
Last update date Feb 02, 2021
Contact name Viviana Piccolo
Organization name European Institute of Oncology (IEO)
Department Department of Experimental Oncology
Lab Gioacchino Natoli Lab
Street address Via Adamello 16
City Milano
State/province Milano
ZIP/Postal code 20139
Country Italy
Platform ID GPL19057
Series (2)
GSE133103 A first exon termination checkpoint that preferentially suppresses extragenic transcription [ChIP-seq Raw W ZC]
GSE133109 A first exon termination checkpoint that preferentially suppresses extragenic transcription
BioSample SAMN12100516
SRA SRX6099385

Supplementary file Size Download File type/resource 284.1 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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