Improve Research Reproducibility A Bio-protocol resource
Concise Method
tooltip

Analysis of RIP-sequencing data

RF Runping Fang
XC Xin Chen
SZ Sicong Zhang
HS Hui Shi
YY Youqiong Ye
HS Hailing Shi
ZZ Zhongyu Zou
PL Peng Li
QG Qing Guo
LM Li Ma
CH Chuan He
SH Suyun Huang
request Request a Protocol
ask Ask a question
Favorite

All samples of RNA-binding protein immunoprecipitation sequencing (RIP-seq) studies were performed by Illumina Hiseq 2500 with single-end 50-bp read length. The deep sequencing data were aligned to human reference genome version 37 (GRCh37) using hisat236 with default setting. After reads were mapped with hisat2, Stringtie37 was used to calculate the read counts of each gene which represent their transcriptional expression level. Then we performed DEseq238 to calculate normalized reads counts in each gene and detect enriched transcripts with a double threshold on the log2-fold change (>1) and the correspondent statistical significance (P value <0.05). Analyzed data are available in Supplementary Data 1. Raw data are available under accession number GSE142828 on the NCBI GEO database.

Copyright and License information: The Author(s) ©2021
Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

Do you have any questions about this protocol?

Post your question to gather feedback from the community. We will also invite the authors of this article to respond.

post Post a Question
0 Q&A