|
| Status |
Public on Mar 02, 2016 |
| Title |
repA_TP3 |
| Sample type |
SRA |
| |
|
| Source name |
trophozoite-stage parasite
|
| Organism |
Plasmodium falciparum |
| Characteristics |
strain: 3D7
hours post-invasion: 18
rna type: capped mRNA
|
| Treatment protocol |
Parasites were synchronized by two consecutive treatments with 5% sorbitol timed 12 hours apart for three or more successive generations and allowed to recover for another parasite asexual blood stage cycle before initiating time point samplings for two biological replicates.
|
| Growth protocol |
P. falciparum strain 3D7 was propagated under standard conditions in RPMI-1640 medium with L-glutamine, supplemented with 50 mg/l hypoxanthine, 25 mM HEPES, 0.25% sodium bicarbonate, 0.01 mg/ml gentamicin and 0.5% Albumax II (Invitrogen, Carlsbad, CA, USA)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated as previously reported (Kyes at al, 2000).
RNA samples were then treated with Terminator 5‘-Phosphate-Dependent Exonuclease. rRNA-depleted RNA was treated with of Calf Intestinal Alkaline Phosphatase (New England BioLabs). CIP-treated RNA was then incubated with Tobacco Acid Pyrophosphatase andincubated overnight with RNA adapters and T4 RNA ligase. RNA was chemically fragmented and reverse transcribed. cDNA second strand was synthesised using biotinylated primers. DNA libraries were constructed using the standard Illumina protocol and amplified with the KAPA HiFi HotStart ReadyMix.
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
5' end capture
|
| Data processing |
Library strategy: 5' cap sequencing
Illumina primers and molecular barcodes were trimmed using the HTSeq package in Python
Reads were aligned to the reference genome (v11) using GMAP (2012-03-23, allowing for the detection of new splicing junctions)
After filtering out multiple alignments, molecular barcodes were used to identify PCR duplicates
Reads were collapsed on their first based pair to be visualized in a bedgraph file
Genome_build: PlasmoDB-11.1_Pfalciparum3D7_Genome
Supplementary_files_format_and_content: Bedgraph format
|
| |
|
| Submission date |
May 18, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Christophe Chabbert |
| Organization name |
EMBL
|
| Street address |
Meyerhofstrasse 1
|
| City |
Heidelberg |
| ZIP/Postal code |
69126 |
| Country |
Germany |
| |
|
| Platform ID |
GPL16607 |
| Series (1) |
| GSE68982 |
Landscape and dynamics of transcription initiation in P. falciparum |
|
| Relations |
| BioSample |
SAMN03700569 |
| SRA |
SRX1032460 |
