GSE215081
Chakkapong_Burudpakdee
2024-08-26
GSE215081- The Myc-Associated Zinc Finger Protein (MAZ) controls STAT1-mediated antiviral response by reshaping epigenome [ChIP-Seq]
samples: ChIP-Seq of HAP1/K562 control cells and MAZ knockdown/knockout cells were generated by deep sequencing in duplicate using Illumina GAIIx. Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for STAT1 and H3K4me3, H3K27Ac in HAP1 cells.
Public on Mar 25, 2024
The objectives of this study are to understand the regulatory roles of MAZ in biological processes using the NGS-deriveed ChIP-seq, DNA-MEDIP-seq and RNA-seq data in HAP1 control cells and MAZ knockout cells. Our comparative analysis of these data generated from the HAP1 control and MAZ KO cells shows that MAZ is required for recruiting STAT1 to its target sites by reshaping epigenetic landscape in the human genome, thereby mediating antiviral response cells.
Illumina HiSeq 2000 (Homo sapiens)
NIH
Xiao T, Li X, Felsenfeld G
Sample analyzed: cell line: HAP1 chip antibody: ab8580 (H3K4me3) treatment: IFNγ treatment time_(hr): 24
#—-Bowtie2 alignment to hg38
bowtie2 -x /home/deviancedev01/bowtie_hg38/index -U SRR21845243_1.fastq -p 22 | samtools view -bS > HAP1_P_IFN_IpH3K4me3.bam
37658998 reads; of these: 37658998 (100.00%) were unpaired; of these: 436065 (1.16%) aligned 0 times 26284801 (69.80%) aligned exactly 1 time 10938132 (29.05%) aligned >1 times 98.84% overall alignment rate
samtools rmdup HAP1_P_IFN_IpH3K4me3.bam HAP1_P_IFN_IpH3K4me3.rmdup.bam samtools sort HAP1_P_IFN_IpH3K4me3.rmdup.bam -o HAP1_P_IFN_IpH3K4me3.rmdup.sorted.bam samtools index HAP1_P_IFN_IpH3K4me3.rmdup.sorted.bam samtools view -b HAP1_P_IFN_IpH3K4me3.rmdup.sorted.bam chr{1..22} > HAP1_P_IFN_IpH3K4me3.rmdup.sorted.cleaned.bam
bowtie2 -x /home/deviancedev01/bowtie_hg38/index -U SRR28027158_1.fastq -p 22 | samtools view -bS > Input_HAP1_P_IFN.bam
39660312 reads; of these: 39660312 (100.00%) were unpaired; of these: 579292 (1.46%) aligned 0 times 26061381 (65.71%) aligned exactly 1 time 13019639 (32.83%) aligned >1 times 98.54% overall alignment rate
samtools rmdup Input_HAP1_P_IFN.bam Input_HAP1_P_IFN.rmdup.bam samtools sort Input_HAP1_P_IFN.rmdup.bam -o Input_HAP1_P_IFN.rmdup.sorted.bam samtools index Input_HAP1_P_IFN.rmdup.sorted.bam samtools view -b Input_HAP1_P_IFN.rmdup.sorted.bam chr{1..22} > Input_HAP1_P_IFN.rmdup.sorted.cleaned.bam
#—-MACS3 peak calls
macs3 callpeak -t HAP1_P_IFN_IpH3K4me3.rmdup.sorted.cleaned.bam -c Input_HAP1_P_IFN.rmdup.sorted.cleaned.bam -g 2913022398 -n GSE215081_hap1_ifny_h3k4me3 -B -q 0.05
INFO @ 26 Aug 2024 13:28:15: [1636 MB] #3 Pileup will be based on sequencing depth in treatment. INFO @ 26 Aug 2024 13:28:15: [1636 MB] #3 Call peaks for each chromosome… INFO @ 26 Aug 2024 13:29:13: [1636 MB] #4 Write output xls file… GSE215081_hap1_ifny_h3k4me3_peaks.xls INFO @ 26 Aug 2024 13:29:13: [1636 MB] #4 Write peak in narrowPeak format file… GSE215081_hap1_ifny_h3k4me3_peaks.narrowPeak INFO @ 26 Aug 2024 13:29:13: [1636 MB] #4 Write summits bed file… GSE215081_hap1_ifny_h3k4me3_summits.bed INFO @ 26 Aug 2024 13:29:13: [1636 MB] Done!
## Loading required package: stats4## Loading required package: BiocGenerics##
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## 'citation("Biobase")', and for packages 'citation("pkgname")'.## ## ChIPseeker v1.41.1 Learn more at https://yulab-smu.top/contribution-knowledge-mining/
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## Please cite:
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## Guangchuang Yu, Li-Gen Wang, and Qing-Yu He. ChIPseeker: an
## R/Bioconductor package for ChIP peak annotation, comparison and
## visualization. Bioinformatics. 2015, 31(14):2382-2383## clusterProfiler v4.12.5 Learn more at https://yulab-smu.top/contribution-knowledge-mining/
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## T Wu, E Hu, S Xu, M Chen, P Guo, Z Dai, T Feng, L Zhou, W Tang, L Zhan,
## X Fu, S Liu, X Bo, and G Yu. clusterProfiler 4.0: A universal
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## If you use ReactomePA in published research, please cite:
## Guangchuang Yu, Qing-Yu He. ReactomePA: an R/Bioconductor package for reactome pathway analysis and visualization. Molecular BioSystems 2016, 12(2):477-479##
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## Pathview is an open source software package distributed under GNU General
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## http://www.gnu.org/licenses/gpl-3.0.html. Particullary, users are required to
## formally cite the original Pathview paper (not just mention it) in publications
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## >> binning method is used...2024-08-26 09:40:13 PM
## >> preparing start_site regions by gene... 2024-08-26 09:40:13 PM
## >> preparing tag matrix by binning... 2024-08-26 09:40:13 PM
## >> preparing promoter regions... 2024-08-26 09:40:32 PM
## >> preparing tag matrix... 2024-08-26 09:40:32 PM
## >> binning method is used...2024-08-26 09:40:32 PM
## >> preparing start_site regions by gene... 2024-08-26 09:40:32 PM
## >> preparing tag matrix by binning... 2024-08-26 09:40:32 PM
## >> generating figure... 2024-08-26 09:40:47 PM
## >> done... 2024-08-26 09:40:47 PM
## >> preparing promoter regions... 2024-08-26 09:41:11 PM
## >> preparing tag matrix... 2024-08-26 09:41:11 PM
## >> binning method is used...2024-08-26 09:41:11 PM
## >> preparing start_site regions by gene... 2024-08-26 09:41:11 PM
## >> preparing tag matrix by binning... 2024-08-26 09:41:11 PM
## >> generating figure... 2024-08-26 09:41:23 PM
## >> done... 2024-08-26 09:41:24 PM
## >> binning method is used...2024-08-26 09:41:47 PM
## >> preparing body regions by gene... 2024-08-26 09:41:47 PM
## >> preparing tag matrix by binning... 2024-08-26 09:41:47 PM
## >> preparing matrix with flank extension from (TSS-3000bp)~(TTS+3000bp)... 2024-08-26 09:41:47 PM
## >> 619 peaks(4.108589%), having lengths smaller than 800bp, are filtered... 2024-08-26 09:41:55 PM
## >> preparing promoter regions... 2024-08-26 09:44:02 PM
## >> preparing tag matrix... 2024-08-26 09:44:02 PM
## >> binning method is used...2024-08-26 09:44:02 PM
## >> preparing body regions by gene... 2024-08-26 09:44:02 PM
## >> preparing tag matrix by binning... 2024-08-26 09:44:02 PM
## >> preparing matrix with flank extension from (TSS-3000bp)~(TTS+3000bp)... 2024-08-26 09:44:02 PM
## >> 619 peaks(4.108589%), having lengths smaller than 800bp, are filtered... 2024-08-26 09:44:07 PM
## >> generating figure... 2024-08-26 09:46:14 PM
## >> done... 2024-08-26 09:46:14 PM
## >> preparing promoter regions... 2024-08-26 09:46:41 PM
## >> preparing tag matrix... 2024-08-26 09:46:41 PM
## >> binning method is used...2024-08-26 09:46:41 PM
## >> preparing body regions by gene... 2024-08-26 09:46:41 PM
## >> preparing tag matrix by binning... 2024-08-26 09:46:41 PM
## >> preparing matrix with flank extension from (TSS-3000bp)~(TTS+3000bp)... 2024-08-26 09:46:42 PM
## >> 649 peaks(4.286941%), having lengths smaller than 800bp, are filtered... 2024-08-26 09:46:44 PM
## >> generating figure... 2024-08-26 09:48:50 PM
## >> done... 2024-08-26 09:48:51 PM## Scale for fill is already present.
## Adding another scale for fill, which will replace the existing scale.
## Warning in cnetplot.enrichResult(x, ...): Use 'color.params = list(foldChange = your_value)' instead of 'foldChange'.
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## The colorEdge parameter will be removed in the next version.## Warning in cnetplot.enrichResult(x, ...): Use 'cex.params = list(gene_node = your_value)' instead of 'cex_gene'.
## The cex_gene parameter will be removed in the next version.## Warning in cnetplot.enrichResult(x, ...): Use 'cex.params = list(gene_label = your_value)' instead of 'cex_label_gene'.
## The cex_label_gene parameter will be removed in the next version.## Warning: ggrepel: 1172 unlabeled data points (too many overlaps). Consider
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## Warning in cnetplot.enrichResult(x, ...): Use 'color.params = list(foldChange = your_value)' instead of 'foldChange'.
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## The colorEdge parameter will be removed in the next version.## Warning in cnetplot.enrichResult(x, ...): Use 'cex.params = list(gene_node = your_value)' instead of 'cex_gene'.
## The cex_gene parameter will be removed in the next version.## Warning in cnetplot.enrichResult(x, ...): Use 'cex.params = list(gene_label = your_value)' instead of 'cex_label_gene'.
## The cex_label_gene parameter will be removed in the next version.## Warning: ggrepel: 1192 unlabeled data points (too many overlaps). Consider
## increasing max.overlaps
## >> preparing features information... 2024-08-26 09:49:42 PM
## >> identifying nearest features... 2024-08-26 09:49:42 PM
## >> calculating distance from peak to TSS... 2024-08-26 09:49:42 PM
## >> assigning genomic annotation... 2024-08-26 09:49:42 PM
## >> adding gene annotation... 2024-08-26 09:49:46 PM## 'select()' returned 1:many mapping between keys and columns## >> assigning chromosome lengths 2024-08-26 09:49:47 PM
## >> done... 2024-08-26 09:49:47 PM
## Warning: Removed 123 rows containing non-finite outside the scale range
## (`stat_count()`).## [1] "653635" "100302278" "100288069" "79854" "643837" "148398"
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