GEO DataSets

(Submitter supplied) The human malaria parasite Plasmodium falciparum has a complex and multi-stage life cycle that requires extensive immune escape, invasion of human liver and blood cells, and transmission through the female Anopholes mosquito. To date, the regulatory elements orchestrating these critical parasite processes remain largely unknown. However, there is mounting evidence across a broad range of species that intergenic long non-coding RNA (lncRNA) and antisense RNA can regulate chromatin state and gene expression. more...

Organism:

Plasmodium falciparum

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL16607

15 Samples

Download data: TXT, XLSX

(Submitter supplied) Mechanisms regulating gene expression in malaria parasites are not well understood. Little is known about how this parasite regulates its gene expression during transition from one developmental stage to another and in response to various environmental conditions. Parasites in a diseased host face environments which differ from the static, well adapted in vitro conditions in culture. Parasites thus need to adapt quickly and effectively to these conditions by establishing transcriptional states which is best suited for better survival. more...

Organism:

Plasmodium falciparum 3D7; Plasmodium falciparum

Type:

Expression profiling by array

Platform:

GPL16484

2 Samples

Download data: TXT

(Submitter supplied) Gene expression in Plasmodium falciparum is tightly regulated to ensure successful propagation of the parasite throughout its complex life cycle. The earliest transcriptomics studies in P. falciparum suggested a cascade of transcriptional activity over the course of the 48-hour intraerythrocytic developmental cycle (IDC); however, the just-in-time transcriptional model has recently been challenged by findings that show the importance of post-transcriptional regulation. more...

Organism:

Plasmodium falciparum

Type:

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

Platforms:

GPL21078 GPL21298

24 Samples

Download data: BED, XLSX

(Submitter supplied) Survey of transcriptional activity across 22.6% of the P. falciparum strain 3D7 genome. 872 protein coding genes and 60 putative P. falciparum lncRNAs identified under developmental regulation during the parasite's pathogenic human blood stage.

Organism:

Plasmodium falciparum 3D7; Plasmodium falciparum

Type:

Expression profiling by genome tiling array; Non-coding RNA profiling by genome tiling array

Platform:

GPL13278

4 Samples

Download data: GFF

(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) Intermediate-size noncoding RNAs (is-ncRNAs) have been shown to play important regulatory roles in the development of several eukaryotic organisms. However, they have not been thoroughly explored in Plasmodium falciparum, which is the most virulent malaria parasite infecting human being. By using Illumina/Solexa paired-end sequencing of an is-ncRNA-specific library, we performed a systematic identification of novel is-ncRNAs in intraerythrocytic P. more...

Organism:

Plasmodium falciparum

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL16789

1 Sample

Download data: TXT

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

Organism:

Fusarium graminearum

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL24502 GPL24501

36 Samples

Download data

(Submitter supplied) Long noncoding RNA (lncRNA) plays important roles in morphological differentiation and development in eukaryotes. In filamentous fungi, however, little is known about lncRNAs and their roles in sexual development. Here we describe sexual stage-induced lncRNAs during the formation of perithecium, the sexual fruiting body of Fusarium graminearum. We identified 547 lncRNAs whose expression were developmental stage-specific; about 40% of them peaked during ascus development, when meiosis occurs. more...

Organism:

Fusarium graminearum

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL24501 GPL24502

24 Samples

Download data: GTF, TAB

(Submitter supplied) Long noncoding RNA (lncRNA) plays important roles in morphological differentiation and development in eukaryotes. In filamentous fungi, however, little is known about lncRNAs and their roles in sexual development. Here we describe sexual stage-induced lncRNAs during the formation of perithecium, the sexual fruiting body of Fusarium graminearum. We identified 547 lncRNAs whose expression were developmental stage-specific; about 40% of them peaked during ascus development, when meiosis occurs. more...

Organism:

Fusarium graminearum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24501

12 Samples

Download data: GTF, TAB

(Submitter supplied) The malaria parasite has a complex lifecycle, including several events of differentiation and stage progression, while actively evading immunity in both its mosquito and human hosts. Important parasite gene expression and regulation during these events remain hidden in rare populations of cells. Here, we combine a capillary-based platform for cell isolation with single-cell RNA-sequencing to transcriptionally profile 165 single infected red blood cells (sc.iRBCs) during the intra- erythrocyte developmental cycle (IDC). more...

Organism:

Plasmodium falciparum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16607

208 Samples

Download data: TXT

(Submitter supplied) Recent advances in transcriptome sequencing have enabled the discovery of thousands of long non-coding RNAs (lncRNAs) across many species. Though several lncRNAs have been shown to play important roles in diverse biological processes, the functions and mechanisms of most lncRNAs remain unknown. Two significant obstacles lie between transcriptome sequencing and functional characterization of lncRNAs: identifying truly non-coding genes from de novo reconstructed transcriptomes, and prioritizing the hundreds of resulting putative lncRNAs for downstream experimental interrogation. more...

Organism:

Homo sapiens; Mus musculus castaneus; Rattus norvegicus; Mus musculus

Type:

Expression profiling by high throughput sequencing

4 related Platforms

9 Samples

Download data: TXT, WIG

(Submitter supplied) Plasmodium vivax is the most geographically widespread human malaria parasite causing approximately 130-435 million infections annually. It is an economic burden in many parts of the world and poses a public health challenge along with the other Plasmodium sp. The biology of this parasite is very little understood. Emerging evidences of severe complications due to infections by this parasite provides an impetus to focus research on the same. more...

Organism:

Plasmodium vivax

Type:

Expression profiling by array

Platform:

GPL16492

2 Samples

Download data: TXT

(Submitter supplied) Here we have designed a full processing pipeline of P. falciparum RNA that innclues RNA preservation, extraction, cDNA synthesis and amplification, globin depletion and final transcriptome readout. To validate the protocol we have analyzed transcriptomes of P. falciaprum samples derived from filed studies as well as 3D7 lab strains. This dataset have been used to establish the best conditions for whole transcriptome amplification protocol. more...

Organism:

Plasmodium falciparum

Type:

Expression profiling by array

Platform:

GPL18893

28 Samples

Download data: GPR

(Submitter supplied) Here we have designed a full processing pipeline of P. falciparum RNA that innclues RNA preservation, extraction, cDNA synthesis and amplification, globin depletion and final transcriptome readout. To validate the protocol we have analyzed transcriptomes of P. falciaprum samples derived from filed studies as well as 3D7 lab strains.

Organism:

Plasmodium falciparum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27825

22 Samples

Download data: TXT

(Submitter supplied) The time course transcriptome of Plasmodium falciparum 3D7 parasite strain was generated by collecting RNA samples every 2 hours during full Intraerythrocytic Developmental Cycle.

Organism:

Plasmodium falciparum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27825

24 Samples

Download data: TXT

(Submitter supplied) The time course transcriptome were generated in Plasmodium falciparum parasite of 3D7 strain by collecting RNA samples every 2 hours during 48 hours of the full intraerythrocytic developmental cycle.

Organism:

Plasmodium falciparum

Type:

Expression profiling by array

Platform:

GPL18893

24 Samples

Download data: GPR

(Submitter supplied) ChIP-seq experiments were performed to profile PfH3.3 (PF3D7_0617900) in the malaria parasite Plasmodium falciparum. Sequencing of ChIP samples showed enrichment of PfH3.3 at GC-rich coding sequences and subtelomeric repetitive regions throughout the intraerythrocytic life cycle and additionally in intergenic regions during trophozoite stages. Also the promoter and the coding sequence of the active and poised var2CSA gene were marked (reference genome Plasmodium falciparum 3D7 from PlasmoDB version 6.1)

Organism:

Plasmodium falciparum

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL16607

12 Samples

Download data: BEDGRAPH

(Submitter supplied) Five healthy Laoshan dairy goats (four years old, third lactation) from Qingdao Laoshan dairy goat primary farm (Shandong Province, China) were used. The mammary gland samples were collected surgically after general anaesthesia using Xylazine Hydrochloride injection solution (Huamu Animal Health Products Co., Ltd. China) at corresponding lactation stage, including early, peak and late lactations.

Organism:

Capra hircus

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL15473

3 Samples

Download data: TXT

(Submitter supplied) We designed a custom microarray to profile the expression and used it to measure the expression of 9929 human lncRNAs manually-annotated by the GENCODE group as part of the ENCODE consortium.

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by array

Platform:

GPL15094

31 Samples

Download data: TXT

(Submitter supplied) This data was generated by ENCODE. If you have questions about the data, contact the submitting laboratory directly (Carrie Davis mailto:davisc@cshl.edu (experimental), Alex Dobin mailto:dobin@cshl.edu (computational), Felix Schlesinger mailto:schlesin@cshl.edu (computational), Tom Gingeras mailto:gingeras@cshl.edu (primary investigator), and Roderic Guigo's group mailto:rguigo@imim.es at the CRG). If you have questions about the Genome Browser track associated with this data, contact ENCODE (mailto:genome@soe.ucsc.edu). These tracks were generate by the ENCODE Consortium. They contain information about human RNAs > 200 nucleotides in length obtained as short reads off the Illumina GAIIx platform. Data is available from biological replicates of several cell lines. In addition to profiling Poly-A+ and Poly-A- RNA from whole cells, we have also gather data from various subcellular compartments. In many cases, there are Cap Analysis of Gene Expression (CAGE, RIKEN Institute) and Small RNA-Seq (<200 nucleotides, CSHL) and Pair-End di-TAG-RNA (PET-RNA, Genome Institute of Singapore) datasets available from the same biological replicates. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL10999 GPL11154 GPL9115

99 Samples

Download data: BAM, BEDRNAELEMENTS, BIGWIG, GFF, GTF, PDF, TXT