GSE120023 Processing Pipeline

OTHER code_examples 5 steps

Publication

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

Cell (2019) — PMID 31251911

Dataset

GSE120023

Pervasive Chromatin-RNA Binding Protein Interactions Enable RNA-based Regulation of Transcription [HiC-Seq]

Warning: Pipeline descriptions and code snippets may be inferred or AI-generated. Use them only as a starting point to guide analysis, and validate before use.

Processing Steps

Generate Jupyter Notebook
  1. 1

    Library strategy: HiC-Seq

    Hi-C
  2. 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. 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).

    PCA
  4. 4

    The interaction matrix was visualized by HiCPlotter (Akdemir and Chin, 2015).

  5. 5

    High confident interactions were defined as those with >3 PET counts and q-value < 0.05 for downstream analysis.

Tools Used

Hi-C
Raw Source Text 
Library strategy: HiC-Seq
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.
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).
The interaction matrix was visualized by HiCPlotter (Akdemir and Chin, 2015).
High confident interactions were defined as those with >3 PET counts and q-value < 0.05 for downstream analysis.
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: MICC
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