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| Status |
Public on Dec 20, 2018 |
| Title |
m6A-seq data analysis of control and PCIF1 knockdown transcriptome |
| Organism |
Homo sapiens |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
Purpose: To identify the in vivo RNA targets of PCIF1, we performed meRIP experiments for PCIF1 KD and control cells using an anti-m6A antibody. We envisioned that the cap-specific PCIF1 should selectively alter the m6Am modification at the 5-terminal region of transcripts. Indeed, we observed a reduction of modification peaks at the 5’-end but not the 3’-UTR regions of mRNA upon PCIF1 KD.
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| Overall design |
Methods: Immunoprecipitated RNA fragments were subjected to library construction using NEBNext® UltraTM Directional RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations. Library sequencing was performed on llumina Hiseq X10 with paired-end 2x150 bp read length. Processed reads were mapped to human genome (hg19, UCSC Genome Browser) using tophat2 aligner (v2.0.13) with default parameters.
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| Contributor(s) |
Zhang M, Sun H, Li K |
| Citation missing |
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| Submission date |
Sep 20, 2018 |
| Last update date |
Mar 20, 2019 |
| Contact name |
Kai Li |
| E-mail(s) |
li_kai@pku.edu.cn
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| Organization name |
Peking University
|
| Department |
School of Life Science
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| Lab |
Yi Lab
|
| Street address |
Yi He Yuan Street No.5
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| City |
BeiJing |
| ZIP/Postal code |
100871 |
| Country |
China |
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| Platforms (1) |
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| Samples (8)
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| Relations |
| BioProject |
PRJNA492247 |
| SRA |
SRP162223 |
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