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GSE240326

GSE GEO
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An in situ method for identification of transcriptome-wide protein-RNA interactions in cells

Organism: Mus musculus
Platform: GPL21103
Samples: 78
Experiment Types:
Other Expression profiling by high throughput sequencing
Submitted: Aug 08 2023
Last Updated: Sep 27 2024
Status: Public on Jun 13 2024
Contact: Brian,,Yee (UCSD)

Relations

SuperSeries of: GSE240014 SuperSeries of: GSE240325 SuperSeries of: GSE240521 SuperSeries of: GSE248461 SuperSeries of: GSE263371 SuperSeries of: GSE263870 BioProject: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA1003311

Summary

This SuperSeries is composed of the SubSeries listed below.

Overall Design

Refer to individual Series

Analysis (6 steps)

View Data Processing
Processing steps for GSE240326
  1. remove adapter with Cutadapt
  2. align to hg38 using STAR 2.4.0 (Homo sapiens) or mm10 using STAR 2.5.2 (Mus musculus)
  3. SAILOR analysis to call C-to-U edits and keep only sites with score >0.5 and edit fraction <80%
  4. FLARE analysis to call C-to-U edit clusters
  5. Intersect the edit clusters from 3 replicates, which yields "*confident_peaks.bed"
  6. Subtract STAMP confident clusters to Buffer only control, which yields "*cleaned_confident_peaks.bed"

Supplementary Files (1)

GSE240326_RAW.tar Download
GEO Samples (78)
GSM7679828 GSM7679829 GSM7679830 GSM7679831 GSM7679832 GSM7679833 GSM7679834 GSM7679835 GSM7679836 GSM7679837 GSM7679838 GSM7679839 GSM7679840 GSM7679841 GSM7679842 GSM7679843 GSM7679844 GSM7679845 GSM7679846 GSM7679847 GSM7679848 GSM7679849 GSM7679850 GSM7679851 GSM7679852 GSM7679853 GSM7679854 GSM7679855 GSM7679856 GSM7679857 GSM7679858 GSM7679859 GSM7679860 GSM7679861 GSM7679862 GSM7679863 GSM7679864 GSM7679865 GSM7679866 GSM7696205 GSM7696206 GSM7699376 GSM7699377 GSM7914703 GSM7914704 GSM7914705 GSM7914706 GSM7914707 GSM7914708 GSM7914709 GSM7914710 GSM7914711 GSM7914712 GSM7914713 GSM7914714 GSM7914715 GSM7914716 GSM8190526 GSM8190527 GSM8190528 GSM8190529 GSM8190530 GSM8190531 GSM8190532 GSM8190533 GSM8190534 GSM8190535 GSM8190536 GSM8190537 GSM8190538 GSM8190539 GSM8190540 GSM8200401 GSM8200402 GSM8200403 GSM8200404 GSM8200405 GSM8200406

Dataset Citations (1)

High-sensitivity in situ capture of endogenous RNA-protein interactions in fixed cells and primary tissues.
PMID 39152130 · 2024 · Nature communications
Qishan Liang, Tao Yu, Eric Kofman, Pratibha Jagannatha, Kevin Rhine, Brian A Yee, Kevin D Corbett, Gene W Yeo

Linked Publications (2)

High-sensitivity in situ capture of endogenous RNA-protein interactions in fixed cells and primary tissues.
Nature communications · 2024
High-sensitivity in situ capture of endogenous RNA-protein interactions in fixed cells and primary tissues.
Nature communications · 2024