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GSE120110

GSE GEO
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Pervasive Chromatin-RNA Binding Protein Interactions Enable RNA-based Regulation of Transcription

Organism: Homo sapiens
Platform: GPL11154
Samples: 152
Experiment Types:
Expression profiling by high throughput sequencing Genome binding/occupancy profiling by high throughput sequencing
Submitted: Sep 18 2018
Last Updated: Sep 26 2019
Status: Public on Jun 27 2019
Contact: Rui,,Xiao (Wuhan University)

Relations

SuperSeries of: GSE120023 SuperSeries of: GSE120104 SuperSeries of: GSE120105 BioProject: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA491670

Summary

This SuperSeries is composed of the SubSeries listed below.

Overall Design

Refer to individual Series

Analysis (5 steps)

View Data Processing
Processing steps for GSE120110
  1. Library strategy: HiC-Seq
  2. The ChIA-PET2 software (Li et al., 2017a) was used for quality control and identification of chromatin interactions with the following parameter setting: -A ACGCGATATCTTATC -B AGTCAGATAAGATAT -s 1 -m 1 -t 4 -k 2 -e 1 -l 15 -S 500 -M "-q 0.05" –C 1.
  3. PCA analysis is then applied to 40-kb resolution interaction matrix generated by HiC-Pro (Servant et al., 2015), and regions of continuous positive or negative PC1 values were used for the identification of A or B compartments (Heinz et al., 2010).
  4. The interaction matrix was visualized by HiCPlotter (Akdemir and Chin, 2015).
  5. High confident interactions were defined as those with >3 PET counts and q-value < 0.05 for downstream analysis.

Supplementary Files (1)

GSE120110_RAW.tar Download
GEO Samples (152)
GSM3391789 GSM3391790 GSM3391791 GSM3391792 GSM3393527 GSM3393528 GSM3393529 GSM3393530 GSM3393531 GSM3393532 GSM3393533 GSM3393534 GSM3393535 GSM3393536 GSM3393537 GSM3393538 GSM3393539 GSM3393540 GSM3393541 GSM3393542 GSM3393543 GSM3393544 GSM3393545 GSM3393546 GSM3393547 GSM3393548 GSM3393549 GSM3393550 GSM3393551 GSM3393552 GSM3393553 GSM3393554 GSM3393555 GSM3393556 GSM3393557 GSM3393558 GSM3393559 GSM3393560 GSM3393561 GSM3393562 GSM3393563 GSM3393564 GSM3393565 GSM3393566 GSM3393567 GSM3393568 GSM3393569 GSM3393570 GSM3393571 GSM3393572 GSM3393573 GSM3393574 GSM3393575 GSM3393576 GSM3393577 GSM3393578 GSM3393579 GSM3393580 GSM3393581 GSM3393582 GSM3393583 GSM3393584 GSM3393585 GSM3393586 GSM3393587 GSM3393588 GSM3393589 GSM3393590 GSM3393591 GSM3393592 GSM3393593 GSM3393594 GSM3393595 GSM3393596 GSM3393597 GSM3393598 GSM3393599 GSM3393600 GSM3393601 GSM3393602 GSM3393603 GSM3393604 GSM3393605 GSM3393606 GSM3393607 GSM3393608 GSM3393609 GSM3393610 GSM3393611 GSM3393612 GSM3393613 GSM3393614 GSM3393615 GSM3393616 GSM3393617 GSM3393618 GSM3393619 GSM3393620 GSM3393621 GSM3393622 GSM3393623 GSM3393624 GSM3393625 GSM3393626 GSM3393627 GSM3393628 GSM3393629 GSM3393630 GSM3393631 GSM3393632 GSM3393633 GSM3393634 GSM3393635 GSM3393636 GSM3393668 GSM3393669 GSM3393670 GSM3393671 GSM3393672 GSM3393673 GSM3393674 GSM3393675 GSM3393676 GSM3393677 GSM3393678 GSM3393679 GSM3393680 GSM3393681 GSM3393682 GSM3393683 GSM3393684 GSM3393685 GSM3393686 GSM3393687 GSM3393688 GSM3393689 GSM3393690 GSM3393691 GSM3393692 GSM3393693 GSM3393694 GSM3393695 GSM3393696 GSM3393697 GSM3393698 GSM3393699 GSM3393700 GSM3393701 GSM3393702 GSM3393703 GSM3393704 GSM3393705

Dataset Citations (1)

Pervasive Chromatin-RNA Binding Protein Interactions Enable RNA-Based Regulation of Transcription.
PMID 31251911 · 2019 · Cell
Rui Xiao, Jia-Yu Chen, Zhengyu Liang, Daji Luo, Geng Chen, Zhi John Lu, Yang Chen, Bing Zhou, Hairi Li, Xian Du, Yang Yang, Mingkui San, Xintao Wei, Wen Liu, Eric Lécuyer, Brenton R Graveley, Gene W Yeo, Christopher B Burge, Michael Q Zhang, Yu Zhou, Xiang-Dong Fu

Linked Publications (1)

Pervasive Chromatin-RNA Binding Protein Interactions Enable RNA-Based Regulation of Transcription.
Cell · 2019