GEO DataSets

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Plasmodium falciparum; Plasmodium yoelii

Type:

Expression profiling by high throughput sequencing; Methylation profiling by high throughput sequencing

Platforms:

GPL26836 GPL29225

36 Samples

Download data: XLS

(Submitter supplied) 5-methylcytosine (m5C) is emerging as an important epi-transcriptome modification involving RNA stability and translation efficiency in various biological processes. However, it remains unclear how m5C contributes to the dynamic regulation of transcriptome during the development of Plasmodium. Here, we identified the presence of 5-methylcytosine (m5C) modification in rodent (P. yoelii) and human (P. more...

Organism:

Plasmodium yoelii; Plasmodium falciparum

Type:

Expression profiling by high throughput sequencing; Methylation profiling by high throughput sequencing

Platforms:

GPL26836 GPL29225

14 Samples

Download data: TXT, XLSX

(Submitter supplied) 5-methylcytosine (m5C) is emerging as an important epi-transcriptome modification involving RNA stability and translation efficiency in various biological processes. However, it remains unclear how m5C contributes to the dynamic regulation of transcriptome during the development of Plasmodium. Here, we identified the presence of 5-methylcytosine (m5C) modification in rodent (P. yoelii) and human (P. more...

Organism:

Plasmodium yoelii

Type:

Expression profiling by high throughput sequencing

Platform:

GPL29225

8 Samples

Download data: TXT

(Submitter supplied) 5-methylcytosine (m5C) is emerging as an important epi-transcriptome modification involving RNA stability and translation efficiency in various biological processes. However, it remains unclear how m5C contributes to the dynamic regulation of transcriptome during the development of Plasmodium. Here, we identified the presence of 5-methylcytosine (m5C) modification in rodent (P. yoelii) and human (P. more...

Organism:

Plasmodium yoelii; Plasmodium falciparum

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL26836 GPL29225

14 Samples

Download data: TXT

(Submitter supplied) For malaria transmission, the parasite must undergo sexual differentiation into mature gametocytes. However, the molecular basis for this critical transition in the parasites life cycle is unknown. Six previously uncharacterized genes, Pfg14.744, Pfg14.745, Pfg14.748, Pfg14.763, Pfg14.752 and Pfg6.6 that are members of a 36 gene Plasmodium falciparum-specific subtelomeric superfamily were found to be expressed in parasites that are committed to sexual development as suggested by co-expression of Pfs16 and Pfg27. more...

Organism:

Plasmodium falciparum

Type:

Expression profiling by array

Platform:

GPL1858

8 Samples

Download data: GPR

(Submitter supplied) Plasmodium falciparum gametocytes undergo 14 days of gametocytogenesis to generate mature, transmissible gametocytes. This timecourse delineates the transcriptional profiles of gametocytes from commitment to maturity.

Organism:

Plasmodium falciparum

Type:

Expression profiling by array

Platform:

GPL15130

16 Samples

Download data: TXT

(Submitter supplied) Malaria pathogenesis results from the asexual replication of Plasmodium falciparum within human red blood cells, which relies on a precisely timed cascade of gene expression over a 48-hour life cycle. However, post-transcriptional control of this hardwired program has been largely unexplored. To this end, we performed a comprehensive characterization of m6A mRNA methylation during the different developmental stages. more...

Organism:

Plasmodium falciparum 3D7

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL25935

14 Samples

Download data: BED, BEDGRAPH, TXT

(Submitter supplied) Recent studies of the Puf family of RNA-binding proteins revealed that besides their traditional roles in translational regulation of mRNAs, some Puf proteins are also involved in ribosome biogenesis by binding rRNA. In this study, we report the role of a Puf-like protein in Plasmodium falciparum (name as PfPuf3) and its ortholog PyPuf3 in Plasmodium yoelii in ribosome biogenesis. Secondary structure prediction suggested that the RNA-binding domain of Puf3 consists of 11 pumilio repeats, similar to human Puf-A/yeast Puf6, which involved in ribosome biogenesis. more...

Organism:

Plasmodium falciparum

Type:

Other

Platform:

GPL21078

4 Samples

Download data: TXT

(Submitter supplied) Purpose: In malaria parasites, the regulation of mRNA translation, storage and degradation is a critical aspect of gene expression, especially during the life stage transition. Since the DEAD-box helicases are involved in RNA metabolism, we wanted to determine whether pfdozi disruption led to altered mRNA abundance in P. falciparum. Methods: In this study, we functionally characterized the DEAD-box RNA helicase PfDOZI in the human malaria parasite Plasmodium falciparum and discovered its functions on mRNA metabolism during development. more...

Organism:

Plasmodium falciparum

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL21078 GPL19269

44 Samples

Download data: FASTA, XLSX

(Submitter supplied) Malaria is spread by the transmission of sexual stage parasites, called gametocytes. However, with Plasmodium falciparum, gametocytes can only be detected in peripheral blood when they are mature and transmissible to a mosquito, which complicates control efforts. Here, we identify the set of genes overexpressed in patient blood samples with high levels of gametocyte-committed ring stage parasites. Expression of all 18 genes was regulated by transcription factor AP2-G, which is required for gametocytogenesis. more...

Organism:

Plasmodium falciparum; Homo sapiens

Type:

Expression profiling by array

Platform:

GPL15130

24 Samples

Download data: TXT

(Submitter supplied) 5-methylcytosine (m5C) is a prevalent base modification in tRNA and rRNA but it also occurs more broadly in the transcriptome, including in mRNA. In pursuit of potential links of m5C with mRNA translation, we performed polysome profiling of human HeLa cell lysates and subjected RNA from resultant fractions to efficient bisulfite conversion followed by RNA sequencing (bsRNA-seq). Bioinformatic filters for rigorous site calling were devised to reduce technical noise. more...

Organism:

Homo sapiens

Type:

Methylation profiling by high throughput sequencing; Other

Platform:

GPL16791

12 Samples

Download data: XLSX

(Submitter supplied) In this GEO submission we include the PA-m6A-seq and PA-m5C-seq datasets for HIV in CEM & 293T cells

Organism:

Human immunodeficiency virus

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL26648

11 Samples

Download data: BED

(Submitter supplied) These data were used to assess gene expression and dynamics between oocyst sporozoites and salivary gland sporozoites for both Plasmodium falciparum and Plasmodium yoelii.

Organism:

Plasmodium falciparum 3D7; Plasmodium yoelii yoelii 17XNL

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL24926 GPL23784

12 Samples

Download data: XLSX

(Submitter supplied) 5-methylcytosine sites of mRNA in BxPC-3, PANC1, and MiaPaCa-2 pancreatic cancer cells at the single-base resolution by whole-transcriptome bisulfite sequencing.

Organism:

Homo sapiens

Type:

Methylation profiling by high throughput sequencing; Other

Platform:

GPL18573

15 Samples

Download data: XLSX

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Plasmodium falciparum

Type:

Expression profiling by array

Platform:

GPL15130

44 Samples

Download data: TXT

(Submitter supplied) Differentiation from asexual blood stages to sexual gametocytes is required for transmission of malaria parasites from the human to the mosquito host. Preventing gametocyte commitment and development would block parasite transmission, but the underlying molecular mechanisms behind these processes remain poorly understood. Here, we report that the ApiAP2 transcription factor, PfAP2-G2 (PF3D7_1408200) plays a critical role in the maturation of Plasmodium falciparum gametocytes. more...

Organism:

Plasmodium falciparum

Type:

Expression profiling by array

Platform:

GPL15130

28 Samples

Download data: TXT

(Submitter supplied) Differentiation from asexual blood stages to sexual gametocytes is required for transmission of malaria parasites from the human to the mosquito host. Preventing gametocyte commitment and development would block parasite transmission, but the underlying molecular mechanisms behind these processes remain poorly understood. Here, we report that the ApiAP2 transcription factor, PfAP2-G2 (PF3D7_1408200) plays a critical role in the maturation of Plasmodium falciparum gametocytes. more...

Organism:

Plasmodium falciparum

Type:

Expression profiling by array

Platform:

GPL15130

16 Samples

Download data: TXT

(Submitter supplied) Differentiation from asexual blood stages to sexual gametocytes is required for transmission of malaria parasites from the human host to mosquitos, where sexual fertilization occurs to complete the lifecycle. Although preventing gametocyte development would block parasite transmission, the molecular mechanisms underlying sexual commitment and gametocyte maturation are still relatively unknown. Previous studies identified an ApiAP2 protein, AP2-G2, which plays a critical role in gametocyte maturation in rodent malaria parasite Plasmodium berghei by acting as the repressor of asexual stage genes in gametocytes. more...

Organism:

Plasmodium falciparum

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL21298

10 Samples

Download data: BIGWIG

(Submitter supplied) To date, total mRNA analysis throughout intraerythrocytic development of the malaria parasite, Plasmodium falciparum, has only revealed abundance profiles of each gene at a given time. Here, we establish a new methodology in Plasmodium falciparum that enables biosynthetic labeleing and capture of sub-population mRNA. As a proof of principle for this novel method, we examine the mRNA dynamics of early gametocyte commitment.

Organism:

Plasmodium falciparum

Type:

Expression profiling by array

Platform:

GPL15130

48 Samples

Download data: TXT

(Submitter supplied) To determine the role of ALBA4 in mRNA homeostasis in Plasmodium parasites, we performed comparative total RNA-seq between a WT-GFP line and an alba4-null line. We performed these experiments at three points in the life cycle - asexual (schizont), sexual (gametocyte), and oocyst sporozoite stages. We found that ALBA4 has a multi-faceted role in mRNA homeostasis, and is involved in mRNA fate determination. more...

Organism:

Plasmodium yoelii

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21940

16 Samples

Download data: XLSX