hTERT-RPE-1: Haas20 Track Settings
 
PDCD4 controls the G1/S-phase transition in a telomerase-immortalized epithelial cell line and affects the expression level and translation of mult... (Haas et al. 2020)   (All Elongating Ribosomes (A-site) tracks)

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     RPF control  Ribosome profiles from elongating ribosomes (SRR10240646, SRR10240645, SRR10240644) (Haas et al. 2020)   Schema 
     RPF PDCD4KD  Ribosome profiles from elongating ribosomes (SRR10240643, SRR10240642, SRR10240641) (Haas et al. 2020)   Schema 

Description

Description fromGSE138533: Knockdown induction: hTERT-RPE-1 cells were transfected either with PDCD4-siRNA or control-siRNA (100 nM) and incubated for 24 h. Induced effects were analyzed by ribosome profiling and RNA-seq in triplicate (IlluminaSequencing).

Methods

Raw sequence data were obtainedfrom NCBI FTP directory(SRP224660). Data from the following samples were processed:

RPF_PDCD4KD Ribosome profiles from elongating ribosomes Homo sapiens(Haas, et al. 2020)
RPF_control Ribosome profiles from elongating ribosomes Homo sapiens(Haas, et al. 2020)

Adapter sequences had already been removed from reads. An alignment to ribosomal RNA was performed using Bowtie, and aligning reads were discarded. An alignment to the hg38 genome assembly was performed using Bowtie, and reads below 25 nt were discarded. An offset of 15 nucleotides was then used to get the corresponding A-site of each read.These tracks contain the uniquely mapping reads.,

References

Haas A, Nilges BS, Leidel SA, Klempnauer KH (2020) PDCD4 controls the G1/S-phase transition in a telomerase-immortalized epithelial cell line and affects the expression level and translation of mult... .PubMed comprises more than 30 million citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites.