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_BSF_DD_Sample1_s |
| Strategy | RNA-Seq |
| Source | TRANSCRIPTOMIC |
| Selection | cDNA |
| Layout | SINGLE |
| Construction Protocol | Parasites were entrained/synchronized in vitro for three days by incubating parasites for 12 hr in darkness and 12 hr under a LED 3W lamp. On the 4th and 5th days, parasites were kept in either these alternating conditions or in constant darkness. Bloodstream forms were grown routinely in HMI-11 at 37°C in 5% CO2. 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 two days. For the alternating light experiment, a LED 3W lamp was used to illuminate the cultures inside the incubator, alternating between light and darkness every 12 hr. Temperature was kept at 37°C and fluctuations were monitored and shown to be less than 0.1°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 | ERS1262062 | ||
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Run | ERR1544469 |
FASTQ
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SRA
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