Experiment Detail
| Title | Illumina HiSeq 2000 sequencing; Time series RNA-seq of temperature-entrained and light-entrained bloodstream and procyclic form Trypanosoma brucei cultures |
| Design Description | Time series RNA-seq of temperature-entrained and light-entrained bloodstream and procyclic form Trypanosoma brucei cultures |
| Organism | Trypanosoma brucei |
Library Description
| Name | TF_PF_WW_Sample6_s |
| Strategy | RNA-Seq |
| Source | TRANSCRIPTOMIC |
| Selection | cDNA |
| Layout | SINGLE |
| Construction Protocol | Differentiation of bloodstream forms to procyclic forms was induced by addition of 6 mM cis-acconitate and a temperature change from 37°C to 28°C. Parasites were entrained/synchronized in vitro for three days by incubating parasites for 12 hr at 22°C and 12 hr at 27°C. On the 4th and 5th days, parasites were kept in either these alternating conditions or at constant 27ºC. Individual cultures of parasites were prepared, adjusting the initial parasite density so that at each time point parasite cultures would be at 10^6 parasites/mL. Samples were collected every 4 hr throughout the day. Temperature varied every 12 h from 23°C to 28°C or remained at constant 28°C. RNA was isolated from 10^7 Trypanosoma brucei cells with TRIzol reagent according to the manufacturer’s instructions (Life Technologies). 1 µg of total RNA was enriched for mRNA using Poly-A beads for RNA-seq according to the manufacturer’s instructions (Invitrogen). The removal of ribosomal RNAs was confirmed on a Bioanalyzer Nano Chip (Agilent Technologies). Sequencing libraries were constructed using TruSeq RNA Sample preparation protocol (Illumina). |
Platform
| Platform | ILLUMINA |
| Instrument Model | Illumina HiSeq 2000 |
Processing
| Base Calls | |
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| Sequence Space | |
| Base Caller | |
Spot Information
| Number of Reads per Spots | 0 |
| Spot Length | 0 |
Read Spec
Navigation
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Submission | ERA676218 |
 FTP
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Study | ERP016547 | ||
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Sample | ERS1262123 | ||
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Run | ERR1544530 |
FASTQ
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SRA
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