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GSE211676

GSE GEO
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RANK ligand converts the NCoR/HDAC3 co-repressor to a PGC1β- and RNA-dependent co-activator of osteoclast gene expression

Organism: Mus musculus
Platform: GPL21103
Samples: 158
Experiment Types:
Genome binding/occupancy profiling by high throughput sequencing Expression profiling by high throughput sequencing Other
Submitted: Aug 19 2022
Last Updated: Sep 12 2023
Status: Public on Aug 22 2022
Contact: Christopher,,Glass (University of California, San Diego)

Relations

SuperSeries of: GSE211671 SuperSeries of: GSE211672 SuperSeries of: GSE211674 SuperSeries of: GSE211675 BioProject: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA871282

Summary

This SuperSeries is composed of the SubSeries listed below.

Overall Design

Refer to individual Series

Analysis (10 steps)

View Data Processing
Processing steps for GSE211676
  1. FASTQ files were mapped to the mm10 mouse reference genome with Bowtie2.
  2. Peaks were called with HOMER (findPeaks) using parameters “-style factor -minDist 200 -size 200”.
  3. After merging these peaks, correlations among replicates from the same cell subset/treatment were evaluated by correlation using tag counts.
  4. The two most highly correlated samples were used for identifying the most robust peaks using the irreproducible discovery rate (IDR) method.
  5. For this step, peaks were called with HOMER’s findPeaks, using parameters “-L 0 -C 0 -fdr 0.9 -minDist 200 -size 200”.
  6. IDR peaks from different conditions involved in a comparison merged with HOMER’s mergePeaks and annotated with HOMER’s annotatePeaks.pl.
  7. The raw tags of all samples which had reasonable correlation were quantified with HOMER (annotatePeaks.pl) using parameter “-noadj”.
  8. Peaks which contained at least 4 tags in at least 1 sample were used to identify differentially bounded peaks (DBP) by DESeq2.
Showing first 8 steps.

Supplementary Files (1)

GSE211676_RAW.tar Download
GEO Samples (158)
GSM6482563 GSM6482564 GSM6482565 GSM6482566 GSM6482567 GSM6482568 GSM6482569 GSM6482570 GSM6482571 GSM6482572 GSM6482573 GSM6482574 GSM6482575 GSM6482576 GSM6482577 GSM6482578 GSM6482579 GSM6482580 GSM6482581 GSM6482582 GSM6482583 GSM6482584 GSM6482585 GSM6482586 GSM6482587 GSM6482588 GSM6482589 GSM6482590 GSM6482591 GSM6482592 GSM6482593 GSM6482594 GSM6482595 GSM6482596 GSM6482597 GSM6482598 GSM6482599 GSM6482600 GSM6482601 GSM6482602 GSM6482603 GSM6482604 GSM6482605 GSM6482606 GSM6482607 GSM6482608 GSM6482609 GSM6482610 GSM6482611 GSM6482612 GSM6482613 GSM6482614 GSM6482615 GSM6482616 GSM6482617 GSM6482618 GSM6482619 GSM6482620 GSM6482621 GSM6482622 GSM6482623 GSM6482624 GSM6482625 GSM6482626 GSM6482627 GSM6482628 GSM6482629 GSM6482630 GSM6482631 GSM6482632 GSM6482633 GSM6482634 GSM6482635 GSM6482636 GSM6482637 GSM6482638 GSM6482639 GSM6482640 GSM6482641 GSM6482642 GSM6482643 GSM6482644 GSM6482645 GSM6482646 GSM6482647 GSM6482648 GSM6482649 GSM6482650 GSM6482651 GSM6482652 GSM6482653 GSM6482654 GSM6482655 GSM6482656 GSM6482657 GSM6482658 GSM6482659 GSM6482660 GSM6482715 GSM6482716 GSM6482717 GSM6482718 GSM6482719 GSM6482720 GSM6482721 GSM6482722 GSM6482723 GSM6482724 GSM6482725 GSM6482726 GSM6482727 GSM6482728 GSM6482729 GSM6482730 GSM6482731 GSM6482732 GSM6482733 GSM6482734 GSM6482735 GSM6482736 GSM6482737 GSM6482738 GSM6482739 GSM6482740 GSM6482741 GSM6482742 GSM6482743 GSM6482744 GSM6482745 GSM6482746 GSM6482747 GSM6482748 GSM6482749 GSM6482750 GSM6482751 GSM6482752 GSM6482753 GSM6482754 GSM6482755 GSM6482756 GSM6482757 GSM6482758 GSM6482759 GSM6482760 GSM6482761 GSM6482762 GSM6482763 GSM6482764 GSM6482765 GSM6482766 GSM6482767 GSM6482768 GSM6482769 GSM6482770 GSM6482771 GSM6482772 GSM6482773 GSM6482774

Linked Publications (1)

RANK ligand converts the NCoR/HDAC3 co-repressor to a PGC1β- and RNA-dependent co-activator of osteoclast gene expression.
Molecular cell · 2023