|
| Status |
Public on Jan 18, 2017 |
| Title |
pfmgrnaS1 |
| Sample type |
SRA |
| |
|
| Source name |
Pf midgut oocysts
|
| Organism |
Plasmodium falciparum |
| Characteristics |
tissue: Anopheles gambiae infected midguts
strain: natural isolate
|
| Treatment protocol |
A. gambiae mosquitoes were maintained under standard insectary conditions (27 ± 2°C, 70 ± 5% relative humidity, 12:12 LD). Two independent experimental infections, biological replicates, were carried out by membrane blood feeding in the laboratory on gametocyte-infected blood from malaria patients in Burkina Faso. Dissection of the midguts and the salivary glands was performed on adult females aged 3-4 days. Tissues were maintained in ice-cold Schneider’s insect culture medium (Sigma-Aldrich) to avoid degradation, and fresh tissues were immediately processed for chromatin and RNA analyses.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Illumina libraries were prepared and sequenced at the HudsonAlpha Institute for Biotechnology, using an Illumina HiSeq2000 sequencer. Standard directional RNA-seq library construction, 50 bp paired end reads with ribosomal reduction (RiboMinus™ Eukaryote Kit, Ambion®).
Total RNA was extracted from fresh mosquito tissues (~50 midguts and ~ 50 salivary glands) using the mirVana™ RNA Isolation Kit (Ambion®) according to the manufacturer’s protocol. Nuclei extraction was performed on formaldehid fixed tissues (~50 midguts and ~ 50 salivary glands) followed by chromatin immunoprecipitation according to previously published protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Reads were trimmed using FASTX-Toolkit based on quality scores on both ends.
ChIP-seq reads were aligned to the Pf3D7 (v25.0) genome assembly using Bowtie version 1.0.0 with the following configuration: -t -m 1
Peak calling of histone modification marks was performed using MACS version 1.4 with the following configuration: -f SAM -g 2.29e+7 -p 1e-5 -s 50 -w --single-profile.
RNA-seq reads were aligned to the PF3D7 (v25.0) genome assembly using TopHat version 2.0.10 with the following configuration: -p 8 --bowtie1 --segment-length 20 --library-type=fr-firststrand --min-intron-length 5 --max-intron-length 1000 -G
Transcript counts per gene were obtained using HTSeq with the following configuration: htseq-count -f bam --stranded=yes -m intersection-nonempty -i ID (Sense), and htseq-count -f bam --stranded=reverse -m intersection-nonempty -i ID (Antisense)
Differential expression on exons was performed using DEXSeq using HTSeq counts considering both paired and unpaired mapped reads
Genome_build: Pf3D7 v25.0 (PlasmoDB)
Supplementary_files_format_and_content: Wig files were generated using MACS 1.4
Supplementary_files_format_and_content: Gene expression normalized count files were generated using HTSeq, DESeq2 and DEXSeq
|
| |
|
| Submission date |
Dec 24, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Elena Gómez-Díaz |
| E-mail(s) |
elegomezdiaz@gmail.com
|
| Organization name |
Spanish National Research Council (CSIC)
|
| Department |
Institute of Parasitology and Biomedicine Lopez-Neyra (IPBLN)
|
| Lab |
Gómez-Díaz Lab
|
| Street address |
Avda. del Conocimiento, 17
|
| City |
Armilla |
| State/province |
Granada |
| ZIP/Postal code |
18100 |
| Country |
Spain |
| |
|
| Platform ID |
GPL16607 |
| Series (1) |
| GSE68667 |
Epigenetic regulation of Plasmodium falciparum adaptive plasticity in the mosquito |
|
| Relations |
| BioSample |
SAMN04370578 |
| SRA |
SRX1502366 |
