Erythroid: Khajuria18 Track Settings
 
Ribosome Levels Selectively Regulate Translation and Lineage Commitment in Human Hematopoiesis. (Khajuria et al. 2018)   (All Elongating Ribosomes (Footprints) tracks)

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     CD34 shLuc RPF  Ribosome coverage data from elongating ribosomes (SRR4450332, SRR4450331) (Khajuria et al. 2018)   Schema 
     CD34 shRPL5 RPF  Ribosome coverage data from elongating ribosomes (SRR4450327, SRR4450328) (Khajuria et al. 2018)   Schema 
     CD34 shRPS19 RPF  Ribosome coverage data from elongating ribosomes (SRR4450329, SRR4450330) (Khajuria et al. 2018)   Schema 

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 coverage data from elongating ribosomes Homo sapiens(Khajuria, et al. 2018)
CD34_shRPS19_RPF Ribosome coverage data from elongating ribosomes Homo sapiens(Khajuria, et al. 2018)
CD34_shRPL5_RPF Ribosome coverage data 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. These tracks contain the uniquely mapping reads.,

References

Khajuria 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.