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| Status |
Public on Dec 02, 2023 |
| Title |
ChIPseq_WSN_24h_rep1_Input |
| Sample type |
SRA |
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| Source name |
Calu3
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| Organism |
Homo sapiens |
| Characteristics |
agent: Influenza
time point: 24h
antibody: none
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| 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).
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
ChIP-seq
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| 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
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| Submission date |
Dec 02, 2020 |
| Last update date |
Dec 02, 2023 |
| Contact name |
Barbara Hummel |
| Organization name |
Max Planck Institute of Immunobiology and Epigenetics
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| Street address |
Stübeweg 51
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| City |
Freiburg |
| ZIP/Postal code |
79108 |
| Country |
Germany |
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| 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. |
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| Relations |
| BioSample |
SAMN16979695 |
| SRA |
SRX9619177 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4952866_Combined_WSN_24h_rep1_Input.inputNorm.bw |
155.2 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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