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Sample GSM4952870 Query DataSets for GSM4952870
Status Public on Dec 02, 2023
Title ChIPseq_WSN_6h_rep1_581_Pol2
Sample type SRA
 
Source name Calu3
Organism Homo sapiens
Characteristics agent: Influenza
time point: 6h
antibody: RNA PolII (RPB1) Cell Signaling 14958
Extracted molecule genomic DNA
Extraction protocol Calu3 cells were infected with Influenza or SARS CoV-2 virus for various time points before harvesting them for chromatin profiling. The ChIP-seq library preparation was done as in Arrigoni et al. Communications Biology (2018).
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina NovaSeq 6000
 
Description ChIP-seq
Data processing ChIP-seq reads were aligned to the human genome build hg38 using the ChIP-seq module from the snakePipes package (Bhardwaj et al., Bioinformatics, 2019). Duplicate and discordant reads were removed. Peak calling was done with MACS2 (model- based analysis of ChIP- Seq) (Zhang et al., Genome Biol, 2008) using "--keep-dup all", "--nomodel", "--extsize". Gene annotations and transcript start site (TSS) information for human genes were from taken from Gencode annotation release 31. Reads overlapping the TSS regions (TSS +/- 100bp) were counted using bedtools2 (Quinlan & Hall, Bioinformatics, 2010). Differential analysis of TSS density was done using DESeq2 (Love et al., Genome Biol, 2014). Size factors were calculated based on the signal in genomic bins of corresponding Input samples similar to (Arrigoni et al., Communications Biology, 2018). Profile plots were generated using deeptools2 (Ramirez et al., Nucleic Acids Res, 2016) using bigwig files that were normalized using the size factors calculated based on the corresponding input samples.
Genome_build: hg38
Supplementary_files_format_and_content: bigwig files with normalized read coverage
 
Submission date Dec 02, 2020
Last update date Dec 02, 2023
Contact name Barbara Hummel
Organization name Max Planck Institute of Immunobiology and Epigenetics
Street address Stübeweg 51
City Freiburg
ZIP/Postal code 79108
Country Germany
 
Platform ID GPL24676
Series (2)
GSE162492 ChIP-seq in Calu3 cells upon SARS-CoV2 infection
GSE162495 SARS-CoV2 causes host transcriptional attenuation through an epigenetic pathway.
Relations
BioSample SAMN16979653
SRA SRX9619181

Supplementary file Size Download File type/resource
GSM4952870_Combined_WSN_6h_rep1_581_Pol2.inputNorm.bw 18.3 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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