Description Description fromGSE89183: (mRNA-seq) RNA-seq for control (shLuc), RPL5 knockdown (shRPL5), RPS19 knockdown (shRPS19), and TSR2 knockdown (shTSR2) was performed for two biological replicates of primary human erythroid cells at Day 7 of in vitro culture. (RPF-seq) Ribosome profiling was similarly performed for shLuc, shRPL5, and shRPS19 in the matching biological replicates.
Methods Raw sequence data were obtainedfrom NCBI FTP directory(SRP092068).
Data from the following samples were processed:
| CD34_shLuc_RPF | Ribosome profiles from elongating ribosomes Homo sapiens(Khajuria, et al. 2018) |
| CD34_shRPS19_RPF | Ribosome profiles from elongating ribosomes Homo sapiens(Khajuria, et al. 2018) |
| CD34_shRPL5_RPF | Ribosome profiles from elongating ribosomes Homo sapiens(Khajuria, et al. 2018) |
Adapter sequence AGATCGGAAGAGCACAC and CAGATCGGAAGAGCACA was removed from reads using Cutadapt 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.,ReferencesKhajuria RK, Munschauer M, Ulirsch JC, Fiorini C, Ludwig LS, McFarland SK, Abdulhay NJ, Specht H, Keshishian H, Mani DR, Jovanovic M, Ellis SR, Fulco CP, Engreitz JM, Schxc3xbctz S, Lian J, Gripp KW, Weinberg OK, Pinkus GS, Gehrke L, Regev A, Lander ES, Gazda HT, Lee WY, Panse VG, Carr SA, Sankaran VG (2018) Ribosome Levels Selectively Regulate Translation and Lineage Commitment in Human Hematopoiesis. .Cell. 2018 Mar 22;173(1):90-103.e19. doi: 10.1016/j.cell.2018.02.036. Epub 2018 Mar 15.
|
|