Details
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Type:
Task
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Status: Closed (View Workflow)
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Priority:
Major
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Resolution: Done
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Affects Version/s: None
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Fix Version/s: None
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Labels:None
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Story Points:1
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Epic Link:
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Sprint:Fall 4 2021 Sep 27 - Oct 8
Description
The first run of the rnaseq pipeline used a samples.csv file as input that indicated the incorrect strand.
The protocol used to synthesis the libraries (see attached) was not strand-specific.
Also, the sample name prefixes are a bit awkward and long. Since every sample name contains the letters "120min" let's shorten the prefixes to:
GENOTYPE_TREATMENT_REPLICATE
Genotypes:
- VF36 (wildtype)
- F3H-OX3 (F3H over-expressing line 3)
- F3H-OX4 (F3H over-expressing line 4)
- are (mutant, anthocyanin reduced)
Treatments (duration 2 hours):
- 28 degrees C for 2 hours (control), harvested at 120 minutes
- 28 degrees C for 30 minutes, then shifted to 34 C (treatment), harvested at 120 minutes
Sample codes:
genotype: VF36, F3H-OX3, F3H-OX4
treatment: C and T
replicate: R1, R2, R3