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GSE173508

GSE GEO
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Discovery and functional interrogation of the virus and host RNA interactome of SARS-CoV-2 proteins

Organism: Homo sapiens
Platform: GPL11154
Samples: 159
Experiment Types:
Expression profiling by high throughput sequencing Other
Submitted: Apr 28 2021
Last Updated: Mar 31 2022
Status: Public on Mar 09 2022
Contact: Gene,,Yeo (UCSD)

Relations

SuperSeries of: GSE173498 SuperSeries of: GSE173507 SuperSeries of: GSE198899 BioProject: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA725849

Summary

This SuperSeries is composed of the SubSeries listed below.

Overall Design

Refer to individual Series

Analysis (19 steps)

View Data Processing
Processing steps for GSE173508
  1. Sequenced reads were reformatted to include randomers in read headers with umi_tools (1.0.0).
  2. Args: --random-seed 1 --bc-pattern NNNNNNNNNN
  3. Reads were then trimmed with cutadapt (1.14).
  4. Args: --match-read-wildcards -O 1 --times 1 -e 0.1 --quality-cutoff 6 -m 18 -a InvRNA*.fasta (fasta sequences can be found at: https://github.com/YeoLab/eclip/tree/master/example/inputs/)
  5. Reads were then trimmed once more with cutadapt (1.14) to remove double-ligation events.
  6. Args: --match-read-wildcards -O 5 --times 1 -e 0.1 --quality-cutoff 6 -m 18 -a InvRNA*.fasta (fasta sequences can be found at: https://github.com/YeoLab/eclip/tree/master/example/inputs/)
  7. Trimmed reads were then mapped with STAR (2.4.0i) against a repeat element database (RepBase 18.05).
  8. Args: --runThreadN 16 \ --genomeDir human_repbase \ --readFilesIn path/to/read1 \ --outFileNamePrefix out_prefix \ --outReadsUnmapped Fastx \ --outSAMtype BAM Unsorted \ --outSAMattributes All \ --outSAMunmapped Within \ --outSAMattrRGline ID:foo \ --outFilterType BySJout \ --outFilterMultimapNmax 30 \ --outFilterMultimapScoreRange 1 \ --outFilterScoreMin 10 \ --alignEndsType EndToEnd
Showing first 8 steps.

Supplementary Files (1)

GSE173508_RAW.tar Download
GEO Samples (159)
GSM5268670 GSM5268671 GSM5268672 GSM5268673 GSM5268674 GSM5268675 GSM5268676 GSM5268677 GSM5268678 GSM5268679 GSM5268680 GSM5268681 GSM5268682 GSM5268683 GSM5268684 GSM5268685 GSM5268686 GSM5268687 GSM5268688 GSM5268689 GSM5268690 GSM5268691 GSM5268692 GSM5268693 GSM5268694 GSM5268695 GSM5268696 GSM5268697 GSM5268698 GSM5268699 GSM5268700 GSM5268701 GSM5268702 GSM5268703 GSM5268704 GSM5268705 GSM5268706 GSM5268707 GSM5268708 GSM5268709 GSM5268710 GSM5268711 GSM5268712 GSM5268713 GSM5268714 GSM5268715 GSM5268716 GSM5268717 GSM5268718 GSM5268719 GSM5268720 GSM5268721 GSM5268722 GSM5268723 GSM5268724 GSM5268725 GSM5268726 GSM5268727 GSM5268728 GSM5268729 GSM5268730 GSM5268731 GSM5268732 GSM5268733 GSM5268734 GSM5268735 GSM5268736 GSM5268737 GSM5268738 GSM5268739 GSM5268740 GSM5268741 GSM5268742 GSM5268743 GSM5268744 GSM5268745 GSM5268746 GSM5268747 GSM5268748 GSM5268749 GSM5268750 GSM5268751 GSM5268752 GSM5268753 GSM5268754 GSM5268755 GSM5268756 GSM5268757 GSM5268758 GSM5268759 GSM5268760 GSM5268761 GSM5268762 GSM5268763 GSM5268764 GSM5268765 GSM5268766 GSM5268767 GSM5268768 GSM5268769 GSM5268770 GSM5268771 GSM5268772 GSM5268773 GSM5268774 GSM5268775 GSM5268776 GSM5268777 GSM5268778 GSM5268779 GSM5268780 GSM5268781 GSM5268782 GSM5268783 GSM5268784 GSM5268785 GSM5268786 GSM5268787 GSM5268788 GSM5268789 GSM5268790 GSM5268791 GSM5268792 GSM5268793 GSM5268794 GSM5268795 GSM5268796 GSM5268797 GSM5268798 GSM5268799 GSM5268800 GSM5268801 GSM5268802 GSM5268803 GSM5268804 GSM5268805 GSM5268806 GSM5268807 GSM5268808 GSM5268809 GSM5268810 GSM5268811 GSM5268812 GSM5268813 GSM5268814 GSM5268815 GSM5268816 GSM5268956 GSM5268957 GSM5268958 GSM5268959 GSM5959183 GSM5959184 GSM5959185 GSM5959186 GSM5959187 GSM5959188 GSM5959189 GSM5959190

Dataset Citations (2)

Discovery and functional interrogation of SARS-CoV-2 protein-RNA interactions.
PMID 35233578 · 2022 · bioRxiv : the preprint server for biology
Joy S Xiang, Jasmine R Mueller, En-Ching Luo, Brian A Yee, Danielle Schafer, Jonathan C Schmok, Frederick E Tan, Katherine Rothamel, Rachael N McVicar, Elizabeth M Kwong, Krysten L Jones, Hsuan-Lin Her, Chun-Yuan Chen, Anthony Q Vu, Wenhao Jin, Samuel S Park, Phuong Le, Kristopher W Brannan, Eric R Kofman, Yanhua Li, Alexandra T Tankka, Kevin D Dong, Yan Song, Aaron F Carlin, Eric L Van Nostrand, Sandra L Leibel, Gene W Yeo
Discovery and functional interrogation of SARS-CoV-2 protein-RNA interactions.
PMID 35313591 · 2022 · Research square
Joy S Xiang, Jasmine R Mueller, En-Ching Luo, Brian A Yee, Danielle Schafer, Jonathan C Schmok, Frederick E Tan, Katherine Rothamel, Rachael N McVicar, Elizabeth M Kwong, Ben A Croker, Krysten L Jones, Hsuan-Lin Her, Chun-Yuan Chen, Anthony Q Vu, Wenhao Jin, Samuel S Park, Phuong Le, Kristopher W Brannan, Eric R Kofman, Yanhua Li, Alexandra T Tankka, Kevin D Dong, Yan Song, Alex E Clark, Aaron F Carlin, Eric L Van Nostrand, Sandra L Leibel, Gene W Yeo

Linked Publications (3)

Genome-Wide Interrogation of SARS-CoV-2 RNA-Protein Interactions Uncovers Hidden Regulatory Sites.
bioRxiv : the preprint server for biology · 2025
Discovery and functional interrogation of SARS-CoV-2 protein-RNA interactions.
Research square · 2022
Discovery and functional interrogation of SARS-CoV-2 protein-RNA interactions.
bioRxiv : the preprint server for biology · 2022