|
Status |
Public on Jan 18, 2017 |
Title |
pfmgh3k4me3 |
Sample type |
SRA |
|
|
Source name |
Pf midgut oocysts
|
Organism |
Plasmodium falciparum |
Characteristics |
tissue: Anopheles gambiae infected midguts strain: natural isolate chip antibody: H3K4me3 (Abcam ab8580)
|
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 |
genomic DNA |
Extraction protocol |
Sequencing libraries were prepared following the protocol described by Bowman et al. BMC Genomics 2013, 14:466 doi:10.1186/1471-2164-14-4662013. ChIP libraries were sequenced at the HudsonAlpha Institute for Biotechnology using an Illumina HiSeq2000 sequencer. 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.
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|
|
Library strategy |
ChIP-Seq |
Library source |
genomic |
Library selection |
ChIP |
Instrument model |
Illumina HiSeq 2000 |
|
|
Description |
Chromatin IP against H3K4me3
|
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
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|
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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 |
SAMN04370569 |
SRA |
SRX1502357 |