DOI: 10.5281/zenodo.7996302
title: Code and data for maximum likelihood estimation (MLE) of P. falciparum age from RNA-seq data

description: The original R code was written by Avi Feller and Jacob Lemieux and is described in this publication:

Lemieux JE, Gomez-Escobar N, Feller A, Carret C, Amambua-Ngwa A, Pinches R, Day F, Kyes SA, Conway DJ, Holmes CC and Newbold CI (2009): Statistical estimation of cell-cycle progression and lineage commitment in Plasmodium falciparum reveals a homogeneous pattern of transcription in ex vivo culture. Proc Natl Acad Sci U S A 106(18), 7559-7564 doi: 10.1073/pnas.0811829106 https://www.pnas.org/doi/full/10.1073/pnas.0811829106

In this deposition, the original R script is adapted for command-line use. For usage instructions, see file "README.md".

Furthermore, this deposition contains RNA-seq data for P. falciparum 3D7 cultured with blood from individuals with high, normal or low iron status (experiment 1) or with blood from a healthy donor in the presence vs. absence of 0.7 µM hepcidin (experiment 2) at 6 – 9 and 26 – 29 hours post erythrocyte invasion (hpi). For more details see publication:

Iron transport pathways in the human malaria parasite Plasmodium falciparum revealed by RNA-sequencing, Wunderlich et al. (biorxiv).

Finally, this deposition contains a variety of pre-processed datasets obtained from the following references:

Bártfai R, Hoeijmakers WA, Salcedo-Amaya AM, Smits AH, Janssen-Megens E, Kaan A, Treeck M, Gilberger TW, Françoijs KJ and Stunnenberg HG (2010): H2A.Z demarcates intergenic regions of the Plasmodium falciparum epigenome that are dynamically marked by H3K9ac and H3K4me3. PLoS Pathog 6(12), e1001223 doi: 10.1371/journal.ppat.1001223

Broadbent KM, Broadbent JC, Ribacke U, Wirth D, Rinn JL and Sabeti PC (2015): Strand-specific RNA sequencing in Plasmodium falciparum malaria identifies developmentally regulated long non-coding RNA and circular RNA. BMC Genomics 16(1), 454 doi: 10.1186/s12864-015-1603-4

López-Barragán MJ, Lemieux J, Quiñones M, Williamson KC, Molina-Cruz A, Cui K, Barillas-Mury C, Zhao K and Su X-z (2011): Directional gene expression and antisense transcripts in sexual and asexual stages of Plasmodium falciparum. BMC Genomics 12(1), 587 doi: 10.1186/1471-2164-12-587

Otto TD, Wilinski D, Assefa S, Keane TM, Sarry LR, Böhme U, Lemieux J, Barrell B, Pain A, Berriman M, Newbold C and Llinás M (2010): New insights into the blood-stage transcriptome of Plasmodium falciparum using RNA-Seq. Mol Microbiol 76(1), 12-24 doi: 10.1111/j.1365-2958.2009.07026.x

Siegel TN, Hon CC, Zhang Q, Lopez-Rubio JJ, Scheidig-Benatar C, Martins RM, Sismeiro O, Coppée JY and Scherf A (2014): Strand-specific RNA-Seq reveals widespread and developmentally regulated transcription of natural antisense transcripts in Plasmodium falciparum. BMC Genomics 15(1), 150 doi: 10.1186/1471-2164-15-150

Wichers JS, Scholz JAM, Strauss J, Witt S, Lill A, Ehnold LI, Neupert N, Liffner B, Lühken R, Petter M, Lorenzen S, Wilson DW, Löw C, Lavazec C, Bruchhaus I, Tannich E, Gilberger TW and Bachmann A (2019): Dissecting the gene expression, localization, membrane topology, and function of the Plasmodium falciparum STEVOR protein family. mBio 10(4),  doi: 10.1128/mBio.01500-19